diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe..237c9ed 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,28 +1,21 @@ { + "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json", "name": "nfcore", - "image": "nfcore/gitpod:latest", - "remoteUser": "gitpod", - "runArgs": ["--privileged"], + "image": "nfcore/devcontainer:latest", - // Configure tool-specific properties. - "customizations": { - // Configure properties specific to VS Code. - "vscode": { - // Set *default* container specific settings.json values on container create. - "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", - "python.formatting.yapfPath": "/opt/conda/bin/yapf", - "python.linting.flake8Path": "/opt/conda/bin/flake8", - "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", - "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" - }, + "remoteUser": "root", + "privileged": true, - // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } + "remoteEnv": { + // Workspace path on the host for mounting with docker-outside-of-docker + "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}" + }, + + "onCreateCommand": "./.devcontainer/setup.sh", + + "hostRequirements": { + "cpus": 4, + "memory": "16gb", + "storage": "32gb" } } diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh new file mode 100755 index 0000000..c0ca3c6 --- /dev/null +++ b/.devcontainer/setup.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +# Customise the terminal command prompt +echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc +echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc +export PROMPT_DIRTRIM=2 +export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] ' + +# Update Nextflow +nextflow self-update + +# Update welcome message +echo "Welcome to the nf-core/datasync devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index dd9ffa5..0000000 --- a/.editorconfig +++ /dev/null @@ -1,37 +0,0 @@ -root = true - -[*] -charset = utf-8 -end_of_line = lf -insert_final_newline = true -trim_trailing_whitespace = true -indent_size = 4 -indent_style = space - -[*.{md,yml,yaml,html,css,scss,js}] -indent_size = 2 - -# These files are edited and tested upstream in nf-core/modules -[/modules/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset -[/subworkflows/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset - -[/assets/email*] -indent_size = unset - -# ignore Readme -[README.md] -indent_style = unset - -# ignore python -[*.{py,md}] -indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index 7ad182e..0000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,123 +0,0 @@ -# nf-core/datasync: Contributing Guidelines - -Hi there! -Many thanks for taking an interest in improving nf-core/datasync. - -We try to manage the required tasks for nf-core/datasync using GitHub issues, you probably came to this page when creating one. -Please use the pre-filled template to save time. - -However, don't be put off by this template - other more general issues and suggestions are welcome! -Contributions to the code are even more welcome ;) - -:::info -If you need help using or modifying nf-core/datasync then the best place to ask is on the nf-core Slack [#datasync](https://nfcore.slack.com/channels/datasync) channel ([join our Slack here](https://nf-co.re/join/slack)). -::: - -## Contribution workflow - -If you'd like to write some code for nf-core/datasync, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-core/datasync issues](https://github.com/nf-core/datasync/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/datasync repository](https://github.com/nf-core/datasync) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged - -If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). - -## Tests - -You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to -receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. - -When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. -Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. - -There are typically two types of tests that run: - -### Lint tests - -`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. - -If any failures or warnings are encountered, please follow the listed URL for more documentation. - -### Pipeline tests - -Each `nf-core` pipeline should be set up with a minimal set of test-data. -`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. -If there are any failures then the automated tests fail. -These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. - -## Patch - -:warning: Only in the unlikely and regretful event of a release happening with a bug. - -- On your own fork, make a new branch `patch` based on `upstream/master`. -- Fix the bug, and bump version (X.Y.Z+1). -- A PR should be made on `master` from patch to directly this particular bug. - -## Getting help - -For further information/help, please consult the [nf-core/datasync documentation](https://nf-co.re/datasync/usage) and don't hesitate to get in touch on the nf-core Slack [#datasync](https://nfcore.slack.com/channels/datasync) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Pipeline contribution conventions - -To make the nf-core/datasync code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. - -### Adding a new step - -If you wish to contribute a new step, please use the following coding standards: - -1. Define the corresponding input channel into your new process from the expected previous process channel -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). -6. Add sanity checks and validation for all relevant parameters. -7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test command in `.github/workflow/ci.yml`. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. -10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. - -### Default values - -Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. - -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. - -### Default processes resource requirements - -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. - -The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. - -### Naming schemes - -Please use the following naming schemes, to make it easy to understand what is going where. - -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` - -### Nextflow version bumping - -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` - -### Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). - -## GitHub Codespaces - -This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. - -To get started: - -- Open the repo in [Codespaces](https://github.com/nf-core/datasync/codespaces) -- Tools installed - - nf-core - - Nextflow - -Devcontainer specs: - -- [DevContainer config](.devcontainer/devcontainer.json) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index e7b641c..fb324ab 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -9,7 +9,6 @@ body: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [nf-core/datasync pipeline documentation](https://nf-co.re/datasync/usage) - - type: textarea id: description attributes: diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index ff8f68a..87aab4d 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,16 +8,16 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/datasync/tree/master/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/datasync/tree/main/docs/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/datasync/tree/master/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/datasync/tree/main/docs/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/datasync _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml new file mode 100644 index 0000000..e2833ee --- /dev/null +++ b/.github/actions/get-shards/action.yml @@ -0,0 +1,69 @@ +name: "Get number of shards" +description: "Get the number of nf-test shards for the current CI job" +inputs: + max_shards: + description: "Maximum number of shards allowed" + required: true + paths: + description: "Component paths to test" + required: false + tags: + description: "Tags to pass as argument for nf-test --tag parameter" + required: false +outputs: + shard: + description: "Array of shard numbers" + value: ${{ steps.shards.outputs.shard }} + total_shards: + description: "Total number of shards" + value: ${{ steps.shards.outputs.total_shards }} +runs: + using: "composite" + steps: + - name: Install nf-test + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 + with: + version: ${{ env.NFT_VER }} + - name: Get number of shards + id: shards + shell: bash + run: | + # Run nf-test with dynamic parameter + nftest_output=$(nf-test test \ + --profile +docker \ + $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \ + --dry-run \ + --ci \ + --changed-since HEAD^) || { + echo "nf-test command failed with exit code $?" + echo "Full output: $nftest_output" + exit 1 + } + echo "nf-test dry-run output: $nftest_output" + + # Default values for shard and total_shards + shard="[]" + total_shards=0 + + # Check if there are related tests + if echo "$nftest_output" | grep -q 'No tests to execute'; then + echo "No related tests found." + else + # Extract the number of related tests + number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p') + if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then + shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} )) + shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .) + total_shards="$shards_to_run" + else + echo "Unexpected output format. Falling back to default values." + fi + fi + + # Write to GitHub Actions outputs + echo "shard=$shard" >> $GITHUB_OUTPUT + echo "total_shards=$total_shards" >> $GITHUB_OUTPUT + + # Debugging output + echo "Final shard array: $shard" + echo "Total number of shards: $total_shards" diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml new file mode 100644 index 0000000..01bb137 --- /dev/null +++ b/.github/actions/nf-test/action.yml @@ -0,0 +1,113 @@ +name: "nf-test Action" +description: "Runs nf-test with common setup steps" +inputs: + profile: + description: "Profile to use" + required: true + shard: + description: "Shard number for this CI job" + required: true + total_shards: + description: "Total number of test shards(NOT the total number of matrix jobs)" + required: true + paths: + description: "Test paths" + required: true + tags: + description: "Tags to pass as argument for nf-test --tag parameter" + required: false +runs: + using: "composite" + steps: + - name: Setup Nextflow + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 + with: + version: "${{ env.NXF_VERSION }}" + + - name: Set up Python + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 + with: + python-version: "3.14" + + - name: Install nf-test + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 + with: + version: "${{ env.NFT_VER }}" + install-pdiff: true + + - name: Setup apptainer + if: contains(inputs.profile, 'singularity') + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 + with: + apptainer-version: 1.4.5 + + - name: Set up Singularity + if: contains(inputs.profile, 'singularity') + shell: bash + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Conda setup + if: contains(inputs.profile, 'conda') + uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4 + with: + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge + channel-priority: strict + conda-remove-defaults: true + + - name: Run nf-test + shell: bash + env: + NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + run: | + nf-test test \ + --profile=+${{ inputs.profile }} \ + $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \ + --ci \ + --changed-since HEAD^ \ + --verbose \ + --tap=test.tap \ + --shard ${{ inputs.shard }}/${{ inputs.total_shards }} + + # Save the absolute path of the test.tap file to the output + echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT + + - name: Generate test summary + if: always() + shell: bash + run: | + # Add header if it doesn't exist (using a token file to track this) + if [ ! -f ".summary_header" ]; then + echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY + echo "" >> $GITHUB_STEP_SUMMARY + echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY + echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY + touch .summary_header + fi + + if [ -f test.tap ]; then + while IFS= read -r line; do + if [[ $line =~ ^ok ]]; then + test_name="${line#ok }" + # Remove the test number from the beginning + test_name="${test_name#* }" + echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + elif [[ $line =~ ^not\ ok ]]; then + test_name="${line#not ok }" + # Remove the test number from the beginning + test_name="${test_name#* }" + echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + fi + done < test.tap + else + echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + fi + + - name: Clean up + if: always() + shell: bash + run: | + sudo rm -rf /home/ubuntu/tests/ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 2b7c8ef..5a8075d 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,39 +1,64 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the main/master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: + workflow_dispatch: + pull_request_review: + types: [submitted] release: types: [published] - workflow_dispatch: + jobs: - run-tower: + run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/datasync' + # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered + if: github.repository == 'nf-core/datasync' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release' runs-on: ubuntu-latest steps: - - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 - # TODO nf-core: You can customise AWS full pipeline tests as required - # Add full size test data (but still relatively small datasets for few samples) - # on the `test_full.config` test runs with only one set of parameters + - name: Set revision variable + id: revision + run: | + echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" + + - name: Launch workflow via Seqera Platform + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/datasync/work-${{ github.sha }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} + revision: ${{ steps.revision.outputs.revision }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/datasync/work-${{ steps.revision.outputs.revision }} + nextflow_config: | + plugins { + id 'nf-slack@0.5.0' + } + slack { + enabled = true + bot { + token = '${{ secrets.NFSLACK_BOT_TOKEN }}' + channel = 'datasync' + } + onStart { + enabled = false + } + onComplete { + message = ':white_check_mark: *datasync/test_full* completed successfully! :tada:' + } + onError { + message = ':x: *datasync/test_full* failed :crying_cat_face:' + } + } parameters: | { - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/datasync/results-${{ github.sha }}" + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/datasync/results-${{ steps.revision.outputs.revision }}" } profiles: test_full - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | tower_action_*.log tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index b93ec43..b9e6efa 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -5,29 +5,29 @@ name: nf-core AWS test on: workflow_dispatch: jobs: - run-tower: + run-platform: name: Run AWS tests if: github.repository == 'nf-core/datasync' runs-on: ubuntu-latest steps: - # Launch workflow using Tower CLI tool action - - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + # Launch workflow using Seqera Platform CLI tool action + - name: Launch workflow via Seqera Platform + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/datasync/work-${{ github.sha }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/datasync/work-${{ github.sha }} parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/datasync/results-test-${{ github.sha }}" + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/datasync/results-test-${{ github.sha }}" } profiles: test - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | tower_action_*.log tower_action_*.json diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 8efcff7..720e16c 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -1,44 +1,62 @@ name: nf-core branch protection -# This workflow is triggered on PRs to master branch on the repository -# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` +# This workflow is triggered on PRs to `main`/`master` branch on the repository +# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev` on: - pull_request_target: - branches: [master] + pull_request: + branches: + - main + - master + +permissions: {} jobs: test: runs-on: ubuntu-latest steps: - # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs if: github.repository == 'nf-core/datasync' + env: + HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }} run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/datasync ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ "$HEAD_REPO" == nf-core/datasync ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] - # If the above check failed, post a comment on the PR explaining the failure - # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - - name: Post PR comment + # If the above check failed, build a comment to be posted by the shared poster workflow + - name: Build PR comment if: failure() - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 - with: - message: | - ## This PR is against the `master` branch :x: + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + BASE_REF: ${{ github.event.pull_request.base.ref }} + HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }} + PR_USER: ${{ github.event.pull_request.user.login }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "branch" > pr-comment/header.txt + cat > pr-comment/comment.md <> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + download: runs-on: ubuntu-latest + needs: configure steps: + - name: Check out pipeline code + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 + + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: - python-version: "3.11" + python-version: "3.14" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 + + - name: Read .nf-core.yml + id: read_yml + run: | + echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT" - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git@dev + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - name: Get the repository name and current branch set as environment variable + - name: Make a cache directory for the container images run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + mkdir -p ./singularity_container_images - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ - --revision ${{ env.REPO_BRANCH }} \ - --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ + --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ + --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} - - name: Run the downloaded pipeline + - name: Inspect container images + run: tree ./singularity_container_images | tee ./container_initial + + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT" + + - name: Run the downloaded pipeline (stub) + id: stub_run_pipeline + continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + - name: Run the downloaded pipeline (stub run not supported) + id: run_pipeline + if: ${{ steps.stub_run_pipeline.outcome == 'failure' }} + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" + + - name: Compare container image counts + id: count_comparison + run: | + if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} + final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images > ./container_afterwards + diff ./container_initial ./container_afterwards + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi + + - name: Upload Nextflow logfile for debugging purposes + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: nextflow_logfile.txt + path: .nextflow.log* + include-hidden-files: true diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix_linting.yml similarity index 71% rename from .github/workflows/fix-linting.yml rename to .github/workflows/fix_linting.yml index e1813a5..8579c6f 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,13 +13,13 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: token: ${{ secrets.nf_core_bot_auth_token }} # indication that the linting is being fixed - name: React on comment - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: eyes @@ -31,30 +31,26 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - # Install and run pre-commit - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 - with: - python-version: 3.11 - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - name: Run pre-commit - id: pre-commit - run: pre-commit run --all-files + # Install and run prek + - name: Run prek + id: prek + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 continue-on-error: true # indication that the linting has finished - name: react if linting finished succesfully - if: steps.pre-commit.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + if: steps.prek.outcome == 'success' + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: "+1" - name: Commit & push changes id: commit-and-push - if: steps.pre-commit.outcome == 'failure' + if: steps.prek.outcome == 'failure' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" @@ -67,21 +63,21 @@ jobs: - name: react if linting errors were fixed id: react-if-fixed if: steps.commit-and-push.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: hooray - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: confused - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: issue-number: ${{ github.event.issue.number }} body: | diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 748b431..277f12f 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,11 +1,8 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: - push: - branches: - - dev pull_request: release: types: [published] @@ -14,45 +11,55 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 - with: - python-version: 3.11 - cache: "pip" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - name: Run pre-commit - run: pre-commit run --all-files + - name: Run prek + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: - python-version: "3.11" + python-version: "3.14" architecture: "x64" + - name: Setup uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install nf-core + run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - name: Run nf-core lint + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} @@ -60,10 +67,28 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: linting-logs path: | lint_log.txt lint_results.md PR_number.txt + + # Build a comment for the shared pr-comment.yml poster to publish on the PR + - name: Prepare PR comment + if: ${{ always() }} + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "lint" > pr-comment/header.txt + [ -f lint_results.md ] && cp lint_results.md pr-comment/comment.md || true + + - name: Upload PR comment artifact + if: ${{ always() }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml deleted file mode 100644 index b706875..0000000 --- a/.github/workflows/linting_comment.yml +++ /dev/null @@ -1,28 +0,0 @@ -name: nf-core linting comment -# This workflow is triggered after the linting action is complete -# It posts an automated comment to the PR, even if the PR is coming from a fork - -on: - workflow_run: - workflows: ["nf-core linting"] - -jobs: - test: - runs-on: ubuntu-latest - steps: - - name: Download lint results - uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 - with: - workflow: linting.yml - workflow_conclusion: completed - - - name: Get PR number - id: pr_number - run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - - - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 - with: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - number: ${{ steps.pr_number.outputs.pr_number }} - path: linting-logs/lint_results.md diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml new file mode 100644 index 0000000..e363215 --- /dev/null +++ b/.github/workflows/nf-test.yml @@ -0,0 +1,201 @@ +name: Run nf-test +on: + pull_request: + paths-ignore: + - "docs/**" + - "**/meta.yml" + - "**/*.md" + - "**/*.png" + - "**/*.svg" + release: + types: [published] + workflow_dispatch: + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + NFT_VER: "0.9.4" + NFT_WORKDIR: "~" + NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + +jobs: + nf-test-changes: + name: nf-test-changes + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-nf-test-changes + - runner=4cpu-linux-x64 + outputs: + shard: ${{ steps.set-shards.outputs.shard }} + total_shards: ${{ steps.set-shards.outputs.total_shards }} + steps: + - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner + run: | + ls -la ./ + rm -rf ./* || true + rm -rf ./.??* || true + ls -la ./ + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + with: + fetch-depth: 0 + + - name: get number of shards + id: set-shards + uses: ./.github/actions/get-shards + env: + NFT_VER: ${{ env.NFT_VER }} + with: + max_shards: 7 + + - name: debug + run: | + echo ${{ steps.set-shards.outputs.shard }} + echo ${{ steps.set-shards.outputs.total_shards }} + + nf-test: + name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}" + needs: [nf-test-changes] + if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-nf-test + - runner=4cpu-linux-x64 + strategy: + fail-fast: false + matrix: + shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} + profile: [conda, docker, singularity] + isMain: + - ${{ github.base_ref == 'master' || github.base_ref == 'main' }} + # Exclude conda and singularity on dev + exclude: + - isMain: false + profile: "conda" + - isMain: false + profile: "singularity" + NXF_VER: + - "25.10.4" + - "latest-everything" + env: + NXF_ANSI_LOG: false + TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} + + steps: + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + with: + fetch-depth: 0 + + - name: Run nf-test + id: run_nf_test + uses: ./.github/actions/nf-test + continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} + env: + NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + NXF_VERSION: ${{ matrix.NXF_VER }} + with: + profile: ${{ matrix.profile }} + shard: ${{ matrix.shard }} + total_shards: ${{ env.TOTAL_SHARDS }} + + - name: Report test status + if: ${{ always() }} + run: | + if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then + echo "::error::Test with ${{ matrix.NXF_VER }} failed" + # Add to workflow summary + echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY + if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then + echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing." + fi + if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + exit 1 + fi + fi + + # continue-on-error keeps latest-everything from failing the job, so it never shows up in + # `needs.nf-test.result` downstream and CI stays green. Surface it via a PR comment instead; + # other NXF_VER failures already fail the job/CI directly, so no comment is needed for those. + - name: Prepare PR comment fragment + if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} + run: | + mkdir -p pr-comment-fragment + echo "* ❌ \`${{ matrix.profile }}\` | \`${{ matrix.NXF_VER }}\` | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" > pr-comment-fragment/fragment.md + + - name: Upload PR comment fragment + if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment-fragment-${{ strategy.job-index }} + path: pr-comment-fragment/ + + confirm-pass: + needs: [nf-test] + if: always() + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-confirm-pass + - runner=2cpu-linux-x64 + steps: + - name: One or more tests failed (excluding latest-everything) + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 + + - name: One or more tests cancelled + if: ${{ contains(needs.*.result, 'cancelled') }} + run: exit 1 + + - name: All tests ok + if: ${{ contains(needs.*.result, 'success') }} + run: exit 0 + + - name: debug-print + if: always() + run: | + echo "::group::DEBUG: `needs` Contents" + echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" + echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" + echo "::endgroup::" + + - name: Download PR comment fragments + if: ${{ always() }} + uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + continue-on-error: true + with: + pattern: pr-comment-fragment-* + path: pr-comment-fragments + merge-multiple: true + + # Build a comment for the shared pr-comment.yml poster to publish on the PR. + # Based on the fragments above (not needs.*.result) so non-blocking failures are still reported. + - name: Prepare PR comment + if: ${{ always() }} + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "nf-test" > pr-comment/header.txt + if [ -d pr-comment-fragments ] && [ -n "$(ls -A pr-comment-fragments)" ]; then + { + echo "## ❌ nf-test failed with latest Nextflow version" + echo "" + echo "> [!NOTE]" + echo "> Tests with Nextflow's latest version failed but it will not cause a CI workflow failure." + echo "> Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing." + echo "" + cat pr-comment-fragments/*.md + echo "" + echo "See the [full run](${RUN_URL}) for details." + } > pr-comment/comment.md + fi + + - name: Upload PR comment artifact + if: ${{ always() }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.github/workflows/pr-comment.yml b/.github/workflows/pr-comment.yml new file mode 100644 index 0000000..ab7b59d --- /dev/null +++ b/.github/workflows/pr-comment.yml @@ -0,0 +1,82 @@ +name: Post PR comment +# Shared, privileged comment poster. +# +# This is the single workflow that runs with a write token. It is triggered +# after any of the listed "producer" workflows complete on a pull request. +# Each producer runs untrusted PR code (if any) with a read-only token and +# uploads a `pr-comment` artifact describing the comment to post; this workflow +# only ever reads that plain-text artifact, so no PR code is executed here. +# +# Artifact contract (uploaded by producers under the name `pr-comment`): +# pr_number.txt - the pull request number +# header.txt - sticky-comment identifier (keeps comment types separate) +# comment.md - the Markdown body (omit the file to post nothing) + +on: + workflow_run: + workflows: + - "nf-core linting" + - "nf-core template version comment" + - "nf-core branch protection" + - "Run nf-test" + +permissions: + actions: read + contents: read + pull-requests: write + +jobs: + post-comment: + runs-on: ubuntu-latest + if: github.event.workflow_run.event == 'pull_request' + steps: + - name: Download PR comment artifact + uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 + with: + run_id: ${{ github.event.workflow_run.id }} + name: pr-comment + path: pr-comment + if_no_artifact_found: ignore + + - name: Read comment metadata + id: meta + run: | + echo "::group::Downloaded pr-comment contents" + ls -la pr-comment 2>/dev/null || echo "No pr-comment/ directory was downloaded." + echo "::endgroup::" + + if [ ! -d pr-comment ]; then + echo "No pr-comment artifact found; nothing to post." + exit 0 + fi + + if [ ! -f pr-comment/comment.md ]; then + echo "Artifact present but no comment.md; nothing to post." + exit 0 + fi + + pr_number=$(cat pr-comment/pr_number.txt) + header=$(cat pr-comment/header.txt) + echo "Found comment.md (header='$header', pr_number='$pr_number')." + + # Guard against anything unexpected ending up in the PR number. + case "$pr_number" in + ''|*[!0-9]*) + echo "Invalid PR number: '$pr_number'" + exit 1 + ;; + esac + + echo "pr_number=$pr_number" >> "$GITHUB_OUTPUT" + echo "header=$header" >> "$GITHUB_OUTPUT" + echo "post=true" >> "$GITHUB_OUTPUT" + echo "Will post comment to PR #${pr_number}." + + - name: Post PR comment + if: steps.meta.outputs.post == 'true' + uses: marocchino/sticky-pull-request-comment@5770ad5eb8f42dd2c4f34da00c94c5381e49af88 # v3.0.5 + with: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + number: ${{ steps.meta.outputs.pr_number }} + header: ${{ steps.meta.outputs.header }} + path: pr-comment/comment.md diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c3674af..4974f44 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,9 +12,13 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - - uses: rzr/fediverse-action@master + - name: get description + id: get_description + run: | + echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT + - uses: rzr/fediverse-action@66c2cbb5b1997666b0e28d597631b6a4f09a2719 # v0.0.6 with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} host: "mstdn.science" # custom host if not "mastodon.social" (default) @@ -22,48 +26,15 @@ jobs: # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release message: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - + ${{ steps.get_description.outputs.description }} Please see the changelog: ${{ github.event.release.html_url }} - ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics - - send-tweet: - runs-on: ubuntu-latest - - steps: - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 - with: - python-version: "3.10" - - name: Install dependencies - run: pip install tweepy==4.14.0 - - name: Send tweet - shell: python - run: | - import os - import tweepy - - client = tweepy.Client( - access_token=os.getenv("TWITTER_ACCESS_TOKEN"), - access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), - consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), - consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), - ) - tweet = os.getenv("TWEET") - client.create_tweet(text=tweet) - env: - TWEET: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} - TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} - TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} - TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} + ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 + - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml new file mode 100644 index 0000000..149e285 --- /dev/null +++ b/.github/workflows/template-version-comment.yml @@ -0,0 +1,60 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: + pull_request: + +permissions: {} + +jobs: + check_template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Read template version from .nf-core.yml + uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core + + - name: Build PR comment if template is outdated + # The fork-controlled version is passed via the environment and only ever + # used as quoted shell data (never interpolated into a command), so it + # cannot be used for script injection. + env: + PR_VERSION: ${{ steps.read_yml.outputs['nf_core_version'] }} + PR_NUMBER: ${{ github.event.pull_request.number }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "template-version" > pr-comment/header.txt + + latest_version=$(nf-core --version | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n1) + + if [ -n "$PR_VERSION" ] && [ -n "$latest_version" ] && [ "$PR_VERSION" != "$latest_version" ]; then + cat > pr-comment/comment.md < [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${PR_VERSION}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview). + EOF + fi + + - name: Upload PR comment artifact + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.gitignore b/.gitignore index 5124c9a..5516a06 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,6 @@ results/ testing/ testing* *.pyc +null/ +.lineage/ +.nf-test* diff --git a/.gitpod.yml b/.gitpod.yml deleted file mode 100644 index 363d5b1..0000000 --- a/.gitpod.yml +++ /dev/null @@ -1,22 +0,0 @@ -image: nfcore/gitpod:latest -tasks: - - name: Update Nextflow and setup pre-commit - command: | - pre-commit install --install-hooks - nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS - -vscode: - extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer # SVG viewer - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.hooks/block_pipeline_outdir.sh b/.hooks/block_pipeline_outdir.sh new file mode 100755 index 0000000..e9ba4f9 --- /dev/null +++ b/.hooks/block_pipeline_outdir.sh @@ -0,0 +1,44 @@ +#!/usr/bin/env bash +# This hook is used to block commits if they include staged files inside a directory +# which also contains a subdirectory called `pipeline_info`. The purpose of this is to +# prevent users from inadvertently committing output from pipeline test runs inside the +# development directory. + +set -e + +status=0 +seen_dirs="" + +while IFS= read -r file; do + # The offending output bundle's root is the ancestor directory that has + # `pipeline_info` as an immediate child, so callers can restore it in one go. + if [[ "$file" == pipeline_info/* ]]; then + top_dir="pipeline_info" + elif [[ "$file" == */pipeline_info/* ]]; then + top_dir="${file%%/pipeline_info/*}" + else + top_dir="" + dir=$(dirname "$file") + while [[ "$dir" != "." && "$dir" != "/" ]]; do + if [[ -d "$dir/pipeline_info" ]]; then + top_dir="$dir" + break + fi + dir=$(dirname "$dir") + done + fi + + if [[ -n "$top_dir" ]]; then + echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file" + status=1 + case "$seen_dirs" in + *"|$top_dir|"*) ;; + *) + echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area." + seen_dirs="$seen_dirs|$top_dir|" + ;; + esac + fi +done < <(git diff --cached --name-only) + +exit "$status" diff --git a/.nf-core.yml b/.nf-core.yml index 3805dc8..046dfb2 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1 +1,19 @@ +lint: + files_exist: + - .github/workflows/linting_comment.yml + files_unchanged: + - .github/workflows/branch.yml + - .github/workflows/linting.yml + - .github/PULL_REQUEST_TEMPLATE.md + multiqc_config: false +nf_core_version: 4.1.0 repository_type: pipeline +template: + author: Alexander Peltzer + description: A simple sysops pipeline that can be used to synchronize, integrity check and permanently archive data. + force: false + is_nfcore: true + name: datasync + org: nf-core + outdir: . + version: 1.0.0 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index af57081..e9503db 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,8 +3,48 @@ repos: rev: "v3.1.0" hooks: - id: prettier - - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + additional_dependencies: + - prettier@3.9.6 + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v6.0.0 hooks: - - id: editorconfig-checker - alias: ec + - id: trailing-whitespace + args: [--markdown-linebreak-ext=md] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/(?!local/).*| + subworkflows/(?!local/).*| + .*\.snap$ + )$ + - id: end-of-file-fixer + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/(?!local/).*| + subworkflows/(?!local/).*| + .*\.snap$ + )$ + - id: check-added-large-files + args: [--maxkb=5000] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + .*\.snap$| + lib/nfcore_external_java_deps.jar$| + docs/.*\.(svg|pdf)$| + assets/.*$ + )$ + - id: check-merge-conflict + - repo: https://github.com/seqeralabs/nf-lint-pre-commit + rev: v0.3.0 + hooks: + - id: nextflow-lint + files: '\.nf$|nextflow\.config$' + args: ["-output", "json"] + - repo: local + hooks: + - id: block-pipeline-outdir + name: Prevent committing output from pipeline test runs to the pipeline code itself + entry: ./.hooks/block_pipeline_outdir.sh + language: script diff --git a/.prettierignore b/.prettierignore index 437d763..63cde50 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,6 +1,4 @@ email_template.html -adaptivecard.json -slackreport.json .nextflow* work/ data/ @@ -10,3 +8,7 @@ testing/ testing* *.pyc bin/ +.nf-test/ +ro-crate-metadata.json +modules/nf-core/ +subworkflows/nf-core/ diff --git a/.prettierrc.yml b/.prettierrc.yml index c81f9a7..07dbd8b 100644 --- a/.prettierrc.yml +++ b/.prettierrc.yml @@ -1 +1,6 @@ printWidth: 120 +tabWidth: 4 +overrides: + - files: "*.{md,yml,yaml,html,css,scss,js,cff}" + options: + tabWidth: 2 diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..a33b527 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "markdown.styles": ["public/vscode_markdown.css"] +} diff --git a/CHANGELOG.md b/CHANGELOG.md index 60dad40..c978e73 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,14 +3,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0dev - [date] +## v1.0.0 - 2026-09-28 Initial release of nf-core/datasync, created with the [nf-core](https://nf-co.re/) template. ### `Added` -### `Fixed` - -### `Dependencies` - -### `Deprecated` +- Samplesheet-driven copying of files and directories between local paths and rclone-supported object storage locations. +- Validation of source data against supplied MD5 and SHA-256 checksum manifests before transfer. +- The ability to copy only files that pass checksum validation, and to download remote files when SHA-256 verification is required. +- Post-transfer comparison of copied data against the source, with detailed rclone status files for each sample. +- A MultiQC report covering the input samplesheet, validation summary, checksum validation, and post-transfer checks. +- A local test profile to explore the pipeline and its outputs. diff --git a/CITATIONS.md b/CITATIONS.md index b2a7707..aaca6d9 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,14 +10,20 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +- [Rclone](https://rclone.org) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + > Craig-Wood, N. (2023). Rclone: Rsync for cloud storage (Vers. 1.65.0). Computer software. Web. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +## R packages + +- [R](https://www.R-project.org/) + + > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. + ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) diff --git a/LICENSE b/LICENSE index ef4eaa2..c86c931 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Alexander Peltzer +Copyright (c) The nf-core/datasync team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 36efe8d..96f62ea 100644 --- a/README.md +++ b/README.md @@ -5,64 +5,76 @@ -[![GitHub Actions CI Status](https://github.com/nf-core/datasync/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/datasync/actions/workflows/ci.yml) +[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/datasync) +[![GitHub Actions CI Status](https://github.com/nf-core/datasync/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/datasync/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/datasync/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/datasync/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/datasync/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) - -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/datasync) - -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23datasync-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/datasync)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/datasync) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23datasync-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/datasync)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction -**nf-core/datasync** is a system operation pipeline that provides several workflows for handling system operation / automation tasks that are commonly helpful for various tasks in large data processing / analysis facilities. This includes: +**nf-core/datasync** is a Nextflow pipeline for copying files and directories between storage locations and documenting their integrity. For every row in an input samplesheet, the pipeline: + +1. validates the source against a supplied MD5 and/or SHA-256 checksum manifest using [`rclone checksum`](https://rclone.org/commands/rclone_checksum/); +2. copies the source to the requested destination with [`rclone copy`](https://rclone.org/); +3. compares the copied data with the source using [`rclone check`](https://rclone.org/commands/rclone_check/); and +4. produces detailed `rclone` status files and a consolidated MultiQC report. + +Sources and destinations may be local paths or object-storage URIs such as Amazon S3, S3-compatible storage, or Azure Blob Storage. HTTP(S) URLs are not currently supported for samplesheet `input` or `output_path` values. -- Data Synchronization & Checksum generation - - Configurable: Can provide YAML file which files to include or exclude from sync - - Checksum backend: Can configure which backend to use for checksum generation (e.g. sha256sum, md5, ...) - - Configurable whether to include (sub-) folders in the sync or not (search for checkpoint files, e.g. has to have DEMUX_DONE that signals a demultiplexing run was finished & successfully copied) -- Data Integrity validation - - Provided with a directory to check, can validate that file(s) found are matching checksums from Synchronization subworkflow -- Data Archival & Deletion - - Can check source and target location for existence of file(s) and decide based on user configurable rules whether files can be considered archived - - Timestamp older than X days - - Checksums match Integrity validation report - - Create empty files to make it obvious that archival was performed - - Optionally: Delete files or create list of files to be deleted for manual deletion process +The current tested use case for this pipeline is transfer between S3 buckets. -The pipeline can be configured by users to execute any of the aforementioned subworkflows and then produces a report using MultiQC custom content that also serves as a report of _what_ was done by the pipeline for documentation purposes. +Pass an `rclone` configuration with `--rclone_config` whenever a source or destination URI needs credentials or provider settings. Samplesheet paths use local paths or standard URIs such as `s3://bucket/path`, not rclone's `remote:path` syntax. For non-S3 layouts, design and validate the provider-specific configuration using the upstream [rclone documentation](https://rclone.org/docs/). -## Usage +![nf-core/datasync metro map](docs/images/datasync_nf-metro.svg) + +## Quick start > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, see the [nf-core environment setup guide](https://nf-co.re/docs/get_started/environment_setup/overview). Nextflow 25.10.4 or later is required. -Now, you can run the pipeline using: +To explore the pipeline outputs before preparing your own data, run the bundled `test` profile with a container profile: ```bash nextflow run nf-core/datasync \ - -profile \ - --input samplesheet.csv \ - --outdir - --sync - --sync_backend 'sha256' - --sync_done true #Creates SYNC_DONE file when done in each folder + -profile test,docker \ + --outdir results ``` -> [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +The `test` profile supplies a small samplesheet and `rclone` configuration automatically. It also enables `--rclone_dry_run`, so no files are actually transferred. This makes it useful for exploring the `rclone/` output folders and `multiqc/multiqc_report.html`; remember that post-copy comparison reports describe whatever is already present at the destination because the dry run does not write transfer data. + +To run the pipeline on your own data, create a samplesheet containing one transfer per row: + +```csv +sample,input,output_path,checksum_md5,checksum_sha +run_001,/data/run_001,s3://archive/runs,/data/manifests/run_001_md5.tsv +reference,/data/reference.fa,/data/references,,/data/manifests/reference_sha256.tsv +``` -For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/datasync/usage) and the [parameter documentation](https://nf-co.re/datasync/parameters). +Then launch the pipeline using: + +```bash +nextflow run nf-core/datasync \ + -r \ + -profile docker \ + --input samplesheet.csv \ + --outdir results \ + --rclone_config /path/to/rclone.conf +``` + +`--rclone_config` is optional only when every source and destination is accessible without a configured rclone remote. See the [`rclone` configuration section](docs/usage.md#configuring-rclone-remotes) for the tested S3-to-S3 use case and guidance on adapting rclone configuration files for other providers. To preview copy operations without transferring data, add `--rclone_dry_run`; note that subsequent comparison reports will then describe the unchanged destination. + +See the [usage documentation](docs/usage.md) for samplesheet rules, destination semantics, remote configuration, and reproducible execution. The complete generated parameter reference is available on the [nf-core pipeline page](https://nf-co.re/datasync/parameters). ## Pipeline output -To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/datasync/results) tab on the nf-core website pipeline page. -For more details about the output files and reports, please refer to the -[output documentation](https://nf-co.re/datasync/output). +Results are written below `--outdir`. See the [output documentation](docs/output.md) for file names and status-code interpretation. ## Credits @@ -70,11 +82,15 @@ nf-core/datasync was originally written by Alexander Peltzer. We thank the following people for their extensive assistance in the development of this pipeline: - +- Julian Schwab +- Gregor Sturm +- Antonia Saracco +- Delfina Terradas +- Anabella Trigila ## Contributions and Support -If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). +If you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md). For further information or help, don't hesitate to get in touch on the [Slack `#datasync` channel](https://nfcore.slack.com/channels/datasync) (you can join with [this invite](https://nf-co.re/join/slack)). @@ -83,8 +99,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `# - - An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json deleted file mode 100644 index 4fb8011..0000000 --- a/assets/adaptivecard.json +++ /dev/null @@ -1,67 +0,0 @@ -{ - "type": "message", - "attachments": [ - { - "contentType": "application/vnd.microsoft.card.adaptive", - "contentUrl": null, - "content": { - "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", - "msteams": { - "width": "Full" - }, - "type": "AdaptiveCard", - "version": "1.2", - "body": [ - { - "type": "TextBlock", - "size": "Large", - "weight": "Bolder", - "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", - "text": "nf-core/datasync v${version} - ${runName}", - "wrap": true - }, - { - "type": "TextBlock", - "spacing": "None", - "text": "Completed at ${dateComplete} (duration: ${duration})", - "isSubtle": true, - "wrap": true - }, - { - "type": "TextBlock", - "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>", - "wrap": true - }, - { - "type": "TextBlock", - "text": "The command used to launch the workflow was as follows:", - "wrap": true - }, - { - "type": "TextBlock", - "text": "${commandLine}", - "isSubtle": true, - "wrap": true - } - ], - "actions": [ - { - "type": "Action.ShowCard", - "title": "Pipeline Configuration", - "card": { - "type": "AdaptiveCard", - "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", - "body": [ - { - "type": "FactSet", - "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %> - ] - } - ] - } - } - ] - } - } - ] -} diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index b7c9849..b42f558 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/datasync Methods Description" section_href: "https://github.com/nf-core/datasync" plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

@@ -19,11 +18,3 @@ data: |
  • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
    • ${tool_bibliography} -
    -
    Notes:
    -
      - ${nodoi_text} -
    • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
      • -
    • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
      • -
    -
    diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index dc1af56..b7a17a9 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/datasync + This report has been generated by the nf-core/datasync analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-datasync-methods-description": order: -1000 @@ -10,6 +10,254 @@ report_section_order: "nf-core-datasync-summary": order: -1002 -export_plots: true +export_plots: false disable_version_detection: true + +custom_content: + order: + - samplesheet + - rclone_exit_codes + - rclone_checksum_md5 + - rclone_checksum_sha + - rclone_check + +custom_data: + samplesheet: + section_name: "Input Samplesheet" + description: > + The input samplesheet lists each sample included in the run, the source path to copy, the destination path, + and the user-provided checksum files used to validate the source data. + plot_type: "table" + file_format: "csv" + headers: + sample: + title: Sample ID + input: + title: Path to copy + output_path: + title: Destination path + checksum_md5: + title: MD5 checksum file + checksum_sha: + title: Sha256 checksum file + + rclone_exit_codes: + section_name: "Validation Summary" + description: > + This table summarises the exit codes returned by `RCLONE_CHECK` and `RCLONE_CHECKSUM` for each processed sample. Reviewing these exit codes + can help identify files that were not successfully validated or where unexpected errors occurred during integrity checking + plot_type: "table" + file_format: "tsv" + headers: + Row: + title: Row + hidden: true + Sample: + title: Sample ID + description: "Sample name from the input samplesheet" + Module: + title: Module + Exit code: + title: Exit Code + description: "Exit code reported by the corresponding Rclone module for each processed Sample ID" + cond_formatting_rules: + success: + - s_eq: "0 - Success" + error: + - s_eq: "1 - Error" + syntax_error: + - s_eq: "2 - Syntax or usage error" + directory_not_found: + - s_eq: "3 - Directory not found" + file_not_found: + - s_eq: "4 - File not found" + temporary_error: + - s_eq: "5 - Temporary error" + less_serious_error: + - s_eq: "6 - Less serious error" + fatal_error: + - s_eq: "7 - Fatal error" + transfer_limit_exceeded: + - s_eq: "8 - Transfer limit exceeded" + no_files_transferred: + - s_eq: "9 - No files transferred" + duration_limit_exceeded: + - s_eq: "10 - Duration limit exceeded" + cond_formatting_colours: + - success: "#5cb85c" + - error: "#d9534f" + - syntax_error: "#f0ad4e" + - directory_not_found: "#f0ad4e" + - file_not_found: "#f0ad4e" + - temporary_error: "#5bc0de" + - less_serious_error: "#5bc0de" + - fatal_error: "#8b0000" + - transfer_limit_exceeded: "#9370db" + - no_files_transferred: "#808080" + - duration_limit_exceeded: "#6f42c1" + + rclone_checksum_md5: + parent_id: source_path_checksum_validation + parent_name: "Source checks" + parent_description: > + This section compares checksums calculated from files at each source path with the expected checksums supplied by the user + in the input samplesheet. This confirms source-file integrity before transfer. + section_name: "MD5 Checksum Validation" + description: "Comparison of the expected MD5 checksums provided in the samplesheet with the observed MD5 checksums of the file(s) found at the specified source path." + plot_type: "table" + file_format: "tsv" + headers: + Status: + title: Result + description: "= Match; - Missing in source; + Missing in destination; * Mismatch; ! Error" + cond_formatting_rules: + match: + - s_eq: "=" + - s_eq: "Match" + missing_source: + - s_eq: "-" + - s_eq: "Missing in source" + missing_destination: + - s_eq: "+" + - s_eq: "Missing in destination" + mismatch: + - s_eq: "*" + - s_eq: "Mismatch" + error: + - s_eq: "!" + - s_eq: "Error" + cond_formatting_colours: + - match: "#5cb85c" + - missing_source: "#f0ad4e" + - missing_destination: "#5bc0de" + - mismatch: "#d9534f" + - error: "#8b0000" + File: + title: File + description: "File checked by rclone" + Sample: + title: Sample + description: "Sample name from the input samplesheet" + Priority: + title: Priority + hidden: true + pconfig: + no_violin: true + defaultsort: + - column: Priority + direction: asc + + rclone_checksum_sha: + parent_id: source_path_checksum_validation + parent_name: "Source checks" + parent_description: > + This section compares checksums calculated from files at each source path with the expected checksums supplied by the user + in the input samplesheet. This confirms source-file integrity before transfer. + section_name: "SHA-256 Checksum Validation" + description: "Comparison of the expected SHA-256 checksums provided in the samplesheet with the observed SHA-256 checksums of the file(s) found at the specified source path." + plot_type: "table" + file_format: "tsv" + headers: + Status: + title: Result + description: "= Match; - Missing in source; + Missing in destination; * Mismatch; ! Error" + cond_formatting_rules: + match: + - s_eq: "=" + - s_eq: "Match" + missing_source: + - s_eq: "-" + - s_eq: "Missing in source" + missing_destination: + - s_eq: "+" + - s_eq: "Missing in destination" + mismatch: + - s_eq: "*" + - s_eq: "Mismatch" + error: + - s_eq: "!" + - s_eq: "Error" + cond_formatting_colours: + - match: "#5cb85c" + - missing_source: "#f0ad4e" + - missing_destination: "#5bc0de" + - mismatch: "#d9534f" + - error: "#8b0000" + File: + title: File + description: "File checked by rclone" + Sample: + title: Sample + description: "Sample name from the input samplesheet" + Priority: + title: Priority + hidden: true + pconfig: + no_violin: true + defaultsort: + - column: Priority + direction: asc + + rclone_check: + parent_id: file_transfer_integrity_check + parent_name: "Post-Transfer Checks" + parent_description: > + This section compares corresponding files at the source and destination paths after the transfer step to confirm that the + destination content is complete and unchanged. + section_name: "Source-Destination Checksum Validation" + description: "Comparison of the checksums of corresponding file(s) in the source input path and the output destination to confirm data integrity following file transfer." + plot_type: "table" + file_format: "tsv" + headers: + Status: + title: Result + description: "= Match; - Missing in source; + Missing in destination; * Mismatch; ! Error" + cond_formatting_rules: + match: + - s_eq: "=" + - s_eq: "Match" + missing_source: + - s_eq: "-" + - s_eq: "Missing in source" + missing_destination: + - s_eq: "+" + - s_eq: "Missing in destination" + mismatch: + - s_eq: "*" + - s_eq: "Mismatch" + error: + - s_eq: "!" + - s_eq: "Error" + cond_formatting_colours: + - match: "#5cb85c" + - missing_source: "#f0ad4e" + - missing_destination: "#5bc0de" + - mismatch: "#d9534f" + - error: "#8b0000" + File: + title: File + description: "File checked by rclone" + Sample: + title: Sample + description: "Sample name from the input samplesheet" + Priority: + title: Priority + hidden: true + pconfig: + no_violin: true + defaultsort: + - column: Priority + direction: asc + +sp: + samplesheet: + fn: "samplesheet.csv" + rclone_exit_codes: + fn: "rclone_exit_codes.tsv" + rclone_checksum_md5: + fn: "*_md5_rclone_checksum_mqc.tsv" + rclone_checksum_sha: + fn: "*_sha_rclone_checksum_mqc.tsv" + rclone_check: + fn: "*_rclone_check_mqc.tsv" diff --git a/assets/multiqc_custom.css b/assets/multiqc_custom.css new file mode 100644 index 0000000..3c56370 --- /dev/null +++ b/assets/multiqc_custom.css @@ -0,0 +1,52 @@ +/* Keep the internal row identifier available to MultiQC without displaying it. */ +#rclone_exit_codes-section-plot_table .rowheader, +#rclone_checksum_md5-plot_table .rowheader, +#rclone_checksum_sha-plot_table .rowheader, +#rclone_check-plot_table .rowheader { + display: none; +} + +/* Distinguish major sections from their result subsections. */ +#samplesheet, +#rclone_exit_codes, +#source_path_checksum_validation, +#file_transfer_integrity_check { + font-size: 2rem; +} + +#rclone_checksum_md5, +#rclone_checksum_sha, +#rclone_check { + color: var(--bs-secondary-color, #6c757d); + font-size: 1.35rem; +} + +/* Fit rclone result tables to the report width and wrap long file paths. */ +#rclone_checksum_md5-plot_table, +#rclone_checksum_sha-plot_table, +#rclone_check-plot_table { + table-layout: auto; + width: 100%; +} + +#rclone_checksum_md5-plot_table .Status, +#rclone_checksum_sha-plot_table .Status, +#rclone_check-plot_table .Status { + white-space: nowrap; + width: 1%; +} + +#rclone_exit_codes-section-plot_table .File .val, +#rclone_checksum_md5-plot_table .File .val, +#rclone_checksum_sha-plot_table .File .val, +#rclone_check-plot_table .File .val { + overflow-wrap: anywhere; + white-space: normal; +} + +#rclone_exit_codes-section-plot_table_container .mqc-table-responsive, +#rclone_checksum_md5-plot_table_container .mqc-table-responsive, +#rclone_checksum_sha-plot_table_container .mqc-table-responsive, +#rclone_check-plot_table_container .mqc-table-responsive { + overflow-x: hidden; +} diff --git a/assets/nf-core-datasync_logo_light.png b/assets/nf-core-datasync_logo_light.png index fa8dbfc..1be8821 100644 Binary files a/assets/nf-core-datasync_logo_light.png and b/assets/nf-core-datasync_logo_light.png differ diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 5f653ab..9abae2c 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,2 @@ -sample,fastq_1,fastq_2 -SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz -SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz, +sample,input,output_path,checksum_md5 +sample,s3://foo/path/to/files/,output_path/data,path/to/checksum.md5 diff --git a/assets/schema_input.json b/assets/schema_input.json index 160d278..6d286fd 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,9 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/nf-core/datasync/master/assets/schema_input.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/nf-core/datasync/main/assets/schema_input.json", "title": "nf-core/datasync pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", + "uniqueEntries": ["sample"], "items": { "type": "object", "properties": { @@ -13,21 +14,54 @@ "errorMessage": "Sample name must be provided and cannot contain spaces", "meta": ["id"] }, - "fastq_1": { + "input": { + "type": "string", + "pattern": "^\\S+$", + "allOf": [ + { + "not": { + "pattern": "^[a-zA-Z][a-zA-Z0-9_.+-]*:(?!//).*$" + } + }, + { + "not": { + "pattern": "^https?://.*$" + } + } + ], + "errorMessage": "Input must be a local path or object-storage URI such as s3://bucket/path; HTTP(S) URLs and rclone remote:path syntax are not supported" + }, + "output_path": { + "type": "string", + "pattern": "^\\S+$", + "allOf": [ + { + "not": { + "pattern": "^[a-zA-Z][a-zA-Z0-9_.+-]*:(?!//).*$" + } + }, + { + "not": { + "pattern": "^https?://.*$" + } + } + ], + "errorMessage": "Output path must be a local path or object-storage URI such as s3://bucket/path; HTTP(S) URLs and rclone remote:path syntax are not supported" + }, + "checksum_md5": { "type": "string", "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + "pattern": "^\\S+\\.(tsv|txt|md5)$", + "errorMessage": "Checksum_md5 cannot contain spaces" }, - "fastq_2": { + "checksum_sha": { "type": "string", "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + "pattern": "^\\S+\\.(tsv|txt|sha256)$", + "errorMessage": "Checksum_sha cannot contain spaces" } }, - "required": ["sample", "fastq_1"] + "required": ["sample", "input", "output_path"], + "anyOf": [{ "required": ["checksum_md5"] }, { "required": ["checksum_sha"] }] } } diff --git a/assets/slackreport.json b/assets/slackreport.json deleted file mode 100644 index 259b1af..0000000 --- a/assets/slackreport.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "attachments": [ - { - "fallback": "Plain-text summary of the attachment.", - "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/datasync ${version} - ${runName}", - "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", - "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", - "fields": [ - { - "title": "Command used to launch the workflow", - "value": "```${commandLine}```", - "short": false - } - <% - if (!success) { %> - , - { - "title": "Full error message", - "value": "```${errorReport}```", - "short": false - }, - { - "title": "Pipeline configuration", - "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>", - "short": false - } - <% } - %> - ], - "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})" - } - ] -} diff --git a/bin/create_test_files.sh b/bin/create_test_files.sh deleted file mode 100644 index ddb0120..0000000 --- a/bin/create_test_files.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash -# This script expects a single folder $1 with several subfolders that then need to be synchronized and checksummed to another location $2 -mkdir -p $1 -mkdir -p $2 -touch $1/DemuxDone #Note this needs to be configured as a pattern to look for in the pipeline configuration, otherwise this trigger won't work. -touch $1/fake_file.fastq.gz -touch $1/fake_file2.fastq.gz -echo "Sync me to another place" > $1/SampleSheet.csv diff --git a/conf/base.config b/conf/base.config index de5a3d9..f65f108 100644 --- a/conf/base.config +++ b/conf/base.config @@ -10,47 +10,48 @@ process { - // TODO nf-core: Check the defaults for all processes - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } - errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104 + (175..177)) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' // Process-specific resource requirements - // NOTE - Please try and re-use the labels below as much as possible. + // NOTE - Please try and reuse the labels below as much as possible. // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. - // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } + } + withLabel:process_low_memory { + memory = { 1.GB * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' @@ -59,7 +60,8 @@ process { errorStrategy = 'retry' maxRetries = 2 } - withName:CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false + withLabel: process_gpu { + ext.use_gpu = { workflow.profile.contains('gpu') } + accelerator = { workflow.profile.contains('gpu') ? 1 : null } } } diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config new file mode 100644 index 0000000..584667d --- /dev/null +++ b/conf/containers_conda_lock_files_amd64.config @@ -0,0 +1,4 @@ +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } } +process { withName: 'RCLONE_CHECK' { conda = 'modules/nf-core/rclone/check/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt' } } +process { withName: 'RCLONE_CHECKSUM' { conda = 'modules/nf-core/rclone/checksum/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt' } } +process { withName: 'RCLONE_COPY' { conda = 'modules/nf-core/rclone/copy/.conda-lock/linux_amd64-bd-ff88b2e0040147be_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config new file mode 100644 index 0000000..028f0ed --- /dev/null +++ b/conf/containers_conda_lock_files_arm64.config @@ -0,0 +1,4 @@ +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } } +process { withName: 'RCLONE_CHECK' { conda = 'modules/nf-core/rclone/check/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt' } } +process { withName: 'RCLONE_CHECKSUM' { conda = 'modules/nf-core/rclone/checksum/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt' } } +process { withName: 'RCLONE_COPY' { conda = 'modules/nf-core/rclone/copy/.conda-lock/linux_arm64-bd-ff88b2e0040147be_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config new file mode 100644 index 0000000..79d0789 --- /dev/null +++ b/conf/containers_docker_amd64.config @@ -0,0 +1,4 @@ +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } } +process { withName: 'RCLONE_CHECK' { container = 'community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97' } } +process { withName: 'RCLONE_CHECKSUM' { container = 'community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97' } } +process { withName: 'RCLONE_COPY' { container = 'community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config new file mode 100644 index 0000000..921367a --- /dev/null +++ b/conf/containers_docker_arm64.config @@ -0,0 +1,4 @@ +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } } +process { withName: 'RCLONE_CHECK' { container = 'community.wave.seqera.io/library/rclone:1.74.3--351f8e39202b129a' } } +process { withName: 'RCLONE_CHECKSUM' { container = 'community.wave.seqera.io/library/rclone:1.74.3--351f8e39202b129a' } } +process { withName: 'RCLONE_COPY' { container = 'community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config new file mode 100644 index 0000000..0c31c94 --- /dev/null +++ b/conf/containers_singularity_https_amd64.config @@ -0,0 +1,4 @@ +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } } +process { withName: 'RCLONE_CHECK' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data' } } +process { withName: 'RCLONE_CHECKSUM' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data' } } +process { withName: 'RCLONE_COPY' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c947c1a7171daf074310295417d0f0afe879275e1543fa5fc2a9711e7c2c72ab/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config new file mode 100644 index 0000000..f480fe7 --- /dev/null +++ b/conf/containers_singularity_https_arm64.config @@ -0,0 +1,4 @@ +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } } +process { withName: 'RCLONE_CHECK' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/de/de06d232599f015aa253f63b84ba2e257bb542810dc11714b88ca9b4045b80ea/data' } } +process { withName: 'RCLONE_CHECKSUM' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/de/de06d232599f015aa253f63b84ba2e257bb542810dc11714b88ca9b4045b80ea/data' } } +process { withName: 'RCLONE_COPY' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c947c1a7171daf074310295417d0f0afe879275e1543fa5fc2a9711e7c2c72ab/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config new file mode 100644 index 0000000..2cf2119 --- /dev/null +++ b/conf/containers_singularity_oras_amd64.config @@ -0,0 +1,4 @@ +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } } +process { withName: 'RCLONE_CHECK' { container = 'oras://community.wave.seqera.io/library/rclone:1.74.3--af6486c6ac506f82' } } +process { withName: 'RCLONE_CHECKSUM' { container = 'oras://community.wave.seqera.io/library/rclone:1.74.3--af6486c6ac506f82' } } +process { withName: 'RCLONE_COPY' { container = 'oras://community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config new file mode 100644 index 0000000..026fe86 --- /dev/null +++ b/conf/containers_singularity_oras_arm64.config @@ -0,0 +1,4 @@ +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } } +process { withName: 'RCLONE_CHECK' { container = 'oras://community.wave.seqera.io/library/rclone:1.74.3--49a53709aa05d28d' } } +process { withName: 'RCLONE_CHECKSUM' { container = 'oras://community.wave.seqera.io/library/rclone:1.74.3--49a53709aa05d28d' } } +process { withName: 'RCLONE_COPY' { container = 'oras://community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be' } } diff --git a/conf/igenomes.config b/conf/igenomes.config deleted file mode 100644 index 3f11437..0000000 --- a/conf/igenomes.config +++ /dev/null @@ -1,440 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for iGenomes paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines reference genomes using iGenome paths. - Can be used by any config that customises the base path using: - $params.igenomes_base / --igenomes_base ----------------------------------------------------------------------------------------- -*/ - -params { - // illumina iGenomes reference file paths - genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" - } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'CHM13' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" - bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" - gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" - mito_name = "chrM" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" - } - 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" - } - 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" - } - 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" - } - 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" - } - 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" - } - } -} diff --git a/conf/modules.config b/conf/modules.config index e3ea8fa..e13b34f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,24 +18,79 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: FASTQC { - ext.args = '--quiet' + withName: 'RCLONE_CHECKSUM' { + tag = { "${meta.id}_${hash}" } + ext.prefix = { "${meta.id}_checksum_${hash}" } + ext.args = { + def base_args = [ + '--no-check-certificate' + ] + if (params.download && meta.check_format == 'sha') { + base_args.add("--download") + } + base_args.join(' ') + } + publishDir = [ + path: { "${params.outdir}/rclone/checksum_before/${meta.id}" }, + mode: params.publish_dir_mode + ] + } + + withName: 'CREATE_FILTER_LIST' { + cpus = 1 + memory = { 100.MB * task.attempt } + } + + withName: 'RCLONE_COPY' { + ext.args = { + def base_args = [ + '--log-level INFO', + '--stats 30s', + '--stats-one-line', + '--stats-log-level INFO', + '--s3-chunk-size 64M', + '--no-check-certificate' + ] + if (params.rclone_dry_run) { + base_args.add('--dry-run') + } + if (params.copy_matching_only) { + base_args.add("--files-from ${filter_file}") + } + base_args.join(' ') + } + publishDir = [ + path: { "${params.outdir}/rclone/copy" }, + mode: params.publish_dir_mode + ] } - withName: CUSTOM_DUMPSOFTWAREVERSIONS { + withName: 'RCLONE_CHECK' { + ext.prefix = { "${meta.id}_check" } + ext.args = { + def base_args = [ + '--no-check-certificate', + '--one-way' + ] + base_args.join(' ') + } publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' + path: { "${params.outdir}/rclone/check_after/${meta.id}" }, + mode: params.publish_dir_mode ] } withName: 'MULTIQC' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } + ext.args = { + def args = ['--custom-css-file */multiqc_custom.css'] + if (params.multiqc_title) { + args.add("--title \"$params.multiqc_title\"") + } + args.join(' ') + } publishDir = [ path: { "${params.outdir}/multiqc" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } diff --git a/conf/test.config b/conf/test.config index d9e3341..f152167 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,20 +10,20 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' - - // Genome references - genome = 'R64-1-1' + input = params.pipelines_testdata_base_path + "test-data/samplesheet.csv" + rclone_config = params.pipelines_testdata_base_path + "test-data/rclone.conf" + rclone_dry_run = true } diff --git a/conf/test_copy.config b/conf/test_copy.config new file mode 100644 index 0000000..bc06271 --- /dev/null +++ b/conf/test_copy.config @@ -0,0 +1,24 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running a real copy test +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a real copy test. + + Use as follows: + nextflow run nf-core/datasync -profile test_copy, --outdir + +---------------------------------------------------------------------------------------- +*/ + +params { + config_profile_name = 'Real copy test profile' + config_profile_description = 'Minimal test dataset to test copying to a local test destination' + + // Input data + input = "${projectDir}/tests/assets/real_copy_samplesheet.csv" + + // Rclone options + rclone_config = params.pipelines_testdata_base_path + "test-data/rclone.conf" + copy_matching_only = true + download = true +} diff --git a/conf/test_full.config b/conf/test_full.config index 159a853..d081678 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,10 +15,10 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + input = params.pipelines_testdata_base_path + "test-data/samplesheet_full.csv" - // Genome references - genome = 'R64-1-1' + //Rclone options + rclone_config = params.pipelines_testdata_base_path + "test-data/rclone.conf" + rclone_dry_run = true + download = true } diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md new file mode 100644 index 0000000..9c5bceb --- /dev/null +++ b/docs/CONTRIBUTING.md @@ -0,0 +1,185 @@ +--- +title: Contributing +markdownPlugin: checklist +--- + +# `nf-core/datasync`: Contributing guidelines + +Hi there! +Thanks for taking an interest in improving nf-core/datasync. + +This page describes the recommended nf-core way to contribute to both nf-core/datasync and nf-core pipelines in general, including: + +- [General contribution guidelines](#general-contribution-guidelines): common procedures or guides across all nf-core pipelines. +- [Pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines): procedures or guides specific to the development conventions of nf-core/datasync. + +> [!NOTE] +> If you need help using or modifying nf-core/datasync, ask on the nf-core Slack [#datasync](https://nfcore.slack.com/channels/datasync) channel ([join our Slack here](https://nf-co.re/join/slack)). + +## General contribution guidelines + +### Contribution quick start + +To contribute code to any nf-core pipeline: + +- [ ] Ensure you have Nextflow, nf-core tools, and nf-test installed. See the [nf-core/tools repository](https://github.com/nf-core/tools) for instructions. +- [ ] Check whether a GitHub [issue](https://github.com/nf-core/datasync/issues) about your idea already exists. If an issue does not exist, create one so that others are aware you are working on it. +- [ ] [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/datasync repository](https://github.com/nf-core/datasync) to your GitHub account. +- [ ] Create a branch on your forked repository and make your changes following [pipeline conventions](#pipeline-contribution-conventions) (if applicable). +- [ ] To fix major bugs, name your branch `patch` and follow the [patch release](#patch-release) process. +- [ ] Update relevant documentation within the `docs/` folder, use nf-core/tools to update `nextflow_schema.json`, and update `CITATIONS.md`. +- [ ] Run and/or update tests. See [Testing](#testing) for more information. +- [ ] [Lint](#lint-tests) your code with nf-core/tools. +- [ ] Submit a pull request (PR) against the `dev` branch and request a review. + +If you are not used to this workflow with Git, see the [GitHub documentation](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or [Git resources](https://try.github.io/) for more information. + +## Use of AI and LLMs + +The nf-core stance on the use of AI and LLMs is that humans are still ultimately responsible for their submitted code, regardless of the tools they use. + +If you’re using AI tools, try to stick by these guidelines: + +- Keep PRs as small and focused as possible +- Avoid any unnecessary changes, such as moving or refactoring code (unless that is the explicit intention of the PR) +- Review all generated code yourself before opening a PR, and ensure that you understand it +- Engage with the community review process and expect to make revisions + +For more detail, see the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team. + +### Getting help + +For further information and help, see the [nf-core/datasync documentation](https://nf-co.re/datasync/usage) or ask on the nf-core [#datasync](https://nfcore.slack.com/channels/datasync) Slack channel ([join our Slack here](https://nf-co.re/join/slack)). + +### GitHub Codespaces + +You can contribute to nf-core/datasync without installing a local development environment on your machine by using [GitHub Codespaces](https://github.com/codespaces). + +[GitHub Codespaces](https://github.com/codespaces) is an online developer environment that runs in your browser, complete with VS Code and a terminal. +Most nf-core repositories include a devcontainer configuration, which creates a GitHub Codespaces environment specifically for Nextflow development. +The environment includes pre-installed nf-core tools, Nextflow, and a few other helpful utilities via a Docker container. + +To get started, open the repository in [Codespaces](https://github.com/nf-core/datasync/codespaces). + +### Testing + +Once you have made your changes, run the pipeline with nf-test to test them locally. +For additional information, use the `--verbose` flag to view the Nextflow console log output. + +```bash +nf-test test --tag test --profile +docker --verbose +``` + +If you have added new functionality, ensure you update the test assertions in the `.nf.test` files in the `tests/` directory. +Update the snapshots with the following command: + +```bash +nf-test test --tag test --profile +docker --verbose --update-snapshots +``` + +When you create a pull request with changes, GitHub Actions will run automatic tests. +Pull requests are typically reviewed when these tests are passing. + +Two types of tests are typically run: + +#### Lint tests + +nf-core has a [set of guidelines](https://nf-co.re/docs/specifications/overview) which all pipelines must follow. +To enforce these, run linting with nf-core/tools: + +```bash +nf-core pipelines lint +``` + +If you encounter failures or warnings, follow the linked documentation printed to screen. +For more information about linting tests, see [nf-core/tools API documentation](https://nf-co.re/docs/nf-core-tools/api_reference/latest/pipeline_lint_tests/actions_awsfulltest). + +#### Pipeline tests + +Each nf-core pipeline should be set up with a minimal set of test data. +GitHub Actions runs the pipeline on this data to ensure it runs through and exits successfully. +If there are any failures then the automated tests fail. +These tests are run with the latest available version of Nextflow and the minimum required version specified in the pipeline code. + +### Patch release + +> [!WARNING] +> Only in the unlikely event of a release that contains a critical bug. + +- [ ] Create a new branch `patch` on your fork based on `upstream/main` or `upstream/master`. +- [ ] Fix the bug and use nf-core/tools to bump the version to the next semantic version, for example, `1.2.3` → `1.2.4`. +- [ ] Open a Pull Request from `patch` directly to `main`/`master` with the changes. + +### Pipeline contribution conventions + +nf-core semi-standardises how you write code and other contributions to make the nf-core/datasync code and processing logic more understandable for new contributors and to ensure quality. + +#### Add a new pipeline step + +To contribute a new step to the pipeline, follow the general nf-core coding procedure. +Please also refer to the [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines): + +- [ ] Define the corresponding [input channel](#channel-naming-schemes) into your new process from the expected previous process channel. +- [ ] Install a module with nf-core/tools, or write a local module (see [default processes resource requirements](#default-processes-resource-requirements)), and add it to the target `.nf`. +- [ ] Define the output channel if needed. Mix the version output channel into `ch_versions` and relevant files into `ch_multiqc`. +- [ ] Add new or updated parameters to `nextflow.config` with a [default value](#default-parameter-values). +- [ ] Add new or updated parameters and relevant help text to `nextflow_schema.json` with [nf-core/tools](#default-parameter-values). +- [ ] Add validation for relevant parameters to the pipeline utilisation section of `utils_nfcore_\_pipeline/main.nf` subworkflow. +- [ ] Perform local tests to validate that the new code works as expected. + - [ ] If applicable, add a new test in the `tests` directory. +- [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate. +- [ ] [Lint](#lint-tests) the code with nf-core/tools. +- [ ] Update any diagrams or pipeline images as necessary. +- [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order. +- [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module. +- [ ] Add a description of the output files and, if relevant, images from the MultiQC report to `docs/output.md`. + +To update the minimum required Nextflow version, see the [Nextflow version bumping](#nextflow-version-bumping) section below. For more information about pipeline contributions, see [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines). + +#### Channel naming schemes + +Use the following naming schemes for channels to make the channel flow easier to understand: + +- Initial process channel: `ch_output_from_` +- Intermediate and terminal channels: `ch__for_` + +#### Default parameter values + +Parameters should be initialised and defined with default values within the `params` scope in `nextflow.config`. +They should also be documented in the pipeline JSON schema. + +To update `nextflow_schema.json`, run: + +```bash +nf-core pipelines schema build +``` + +The schema builder interface that loads in your browser should automatically update the defaults in the parameter documentation. + +#### Default processes resource requirements + +If you write a local module, specify a default set of resource requirements for the process. + +Sensible defaults for process resource requirements (CPUs, memory, time) should be defined in `conf/base.config`. +Specify these with generic `withLabel:` selectors, so they can be shared across multiple processes and steps of the pipeline. + +nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config). +These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements. + +Values assigned within these labels can be dynamically passed to a tool using the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). + +#### Nextflow version bumping + +If you use a new feature from core Nextflow, bump the minimum required Nextflow version in the pipeline with: + +```bash +nf-core pipelines bump-version --nextflow . +``` + +#### Images and figures guidelines + +If you update images or graphics, follow the nf-core [style guidelines](https://nf-co.re/docs/community/brand/workflow-schematics). + +## Pipeline specific contribution guidelines + +Pipeline-specific changes should include focused updates to the pipeline code, schema, documentation, and nf-test coverage where behaviour changes. diff --git a/docs/images/datasync-multiqc-checksum-md5.png b/docs/images/datasync-multiqc-checksum-md5.png new file mode 100644 index 0000000..42968b7 Binary files /dev/null and b/docs/images/datasync-multiqc-checksum-md5.png differ diff --git a/docs/images/datasync-multiqc-exit-code-table.png b/docs/images/datasync-multiqc-exit-code-table.png new file mode 100644 index 0000000..56d0c60 Binary files /dev/null and b/docs/images/datasync-multiqc-exit-code-table.png differ diff --git a/docs/images/datasync-multiqc-post-transfer-check.png b/docs/images/datasync-multiqc-post-transfer-check.png new file mode 100644 index 0000000..22014f3 Binary files /dev/null and b/docs/images/datasync-multiqc-post-transfer-check.png differ diff --git a/docs/images/datasync-nf-metro.mmd b/docs/images/datasync-nf-metro.mmd new file mode 100644 index 0000000..c4558dd --- /dev/null +++ b/docs/images/datasync-nf-metro.mmd @@ -0,0 +1,33 @@ +%%metro title: nf-core/datasync +%%metro mode: dark +%%metro style: nfcore +%%metro diamond_style: symmetric +%%metro line: main | Pipeline | #4CAF50 + +%%metro file: ref_in | CSV | Input\nSamplesheet | banner +%%metro file: reads_in | Config | Rclone\nConfig | banner +%%metro file: report_out | HTML | Report | banner +%%metro grid: datasync | 0,0 + +graph LR + subgraph datasync [Datasync pipeline] + ref_in[Input] + reads_in[ ] + node1[Rclone\nChecksum] + node2[Create\nFilter List] + node3[Rclone\nCheck] + node4[Rclone\nCopy] + node5[MultiQC] + Rclone\nChecksum[Rclone\nChecksum] + ref_in -->|main| Rclone\nChecksum + reads_in -->|main| Rclone\nChecksum + report_out[Output] + ref_in -->|main| node1 + reads_in -->|main| node1 + node1 -->|main| node2 + node2 -->|main| node4 + node4 -->|main| node3 + node3 -->|main| node5 + node1 -->|main| node4 + node5 -->|main| report_out + end diff --git a/docs/images/datasync_nf-metro.svg b/docs/images/datasync_nf-metro.svg new file mode 100644 index 0000000..62f95c3 --- /dev/null +++ b/docs/images/datasync_nf-metro.svg @@ -0,0 +1,98 @@ + + + + +{"groups":[{"color":"#4CAF50","id":"main","label":"Pipeline"}],"height":419,"match":{"flags":"i","target":"fqProcessName","type":"regex"},"nodes":[{"groups":["main"],"h":10.0,"id":"ref_in","label":"Input","patterns":[],"r":5.0,"region":"datasync","rx":5.0,"w":10.0,"x":80.0,"y":133.6},{"groups":["main"],"h":10.0,"id":"reads_in","label":"reads_in","patterns":[],"r":5.0,"region":"datasync","rx":5.0,"w":10.0,"x":80.0,"y":267.2},{"groups":["main"],"h":10.0,"id":"node1","label":"Rclone\nChecksum","patterns":[],"r":5.0,"region":"datasync","rx":5.0,"w":10.0,"x":176.0,"y":200.4},{"groups":["main"],"h":10.0,"id":"node2","label":"Create\nFilter 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+RcloneChecksum + +CreateFilter List + +RcloneCopy + +RcloneCheck + +MultiQC + + +Pipeline +created with nf-metro v2.0.0 + diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 361d0e4..0000000 Binary files a/docs/images/mqc_fastqc_adapter.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png deleted file mode 100755 index cb39ebb..0000000 Binary files a/docs/images/mqc_fastqc_counts.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png deleted file mode 100755 index a4b89bf..0000000 Binary files a/docs/images/mqc_fastqc_quality.png and /dev/null differ diff --git a/docs/images/nf-core-datasync_logo_dark.png b/docs/images/nf-core-datasync_logo_dark.png index e1454b9..41d5173 100644 Binary files a/docs/images/nf-core-datasync_logo_dark.png and b/docs/images/nf-core-datasync_logo_dark.png differ diff --git a/docs/images/nf-core-datasync_logo_light.png b/docs/images/nf-core-datasync_logo_light.png index 3be1053..31788eb 100644 Binary files a/docs/images/nf-core-datasync_logo_light.png and b/docs/images/nf-core-datasync_logo_light.png differ diff --git a/docs/output.md b/docs/output.md index 1c847a5..b37a1d7 100644 --- a/docs/output.md +++ b/docs/output.md @@ -2,70 +2,147 @@ ## Introduction -This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. +This document describes the reports produced by nf-core/datasync. Paths below are relative to the directory supplied with `--outdir`. + +> [!IMPORTANT] +> The copied payload is written to each samplesheet row's `output_path`. It is not placed in `--outdir` unless `output_path` explicitly points to the same path as the one specified for `--outdir`. + +## Output overview + +```text +/ +├── rclone/ +│ ├── copy/ +│ │ └── -rclone-copy.log +│ ├── checksum_before/ +│ │ └── / +│ │ ├── .combined.txt +│ │ ├── .match.txt +│ │ ├── .differ.txt +│ │ ├── .missing_on_dst.txt +│ │ ├── .missing_on_src.txt +│ │ └── .error.txt +│ └── check_after/ +│ └── / +│ ├── .combined.txt +│ ├── .match.txt +│ ├── .differ.txt +│ ├── .missing_on_dst.txt +│ ├── .missing_on_src.txt +│ └── .error.txt +├── multiqc/ +│ ├── multiqc_report.html +│ └── multiqc_data/ +└── pipeline_info/ + ├── nf_core_datasync_software_mqc_versions.yml + └── execution_* / pipeline_dag_* +``` + +The `rclone/` directory is split by module stage. Copy logs are published to `rclone/copy/`, pre-copy checksum validation reports are published to `rclone/checksum_before//`, and post-copy source-to-destination comparison reports are published to `rclone/check_after//`. The `` directory name is taken from the `sample` value in the samplesheet row. + +## `rclone` directory -The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. +
    +Output files + +- `rclone/copy/` + - `-rclone-copy.log`: informational log from the copy operation. +- `rclone/checksum_before//` + - `.combined.txt`: combined pre-copy checksum-validation status, one path per line. + - `.match.txt`: paths whose content matched the supplied checksum manifest (`=`). + - `.differ.txt`: paths present in the source and manifest but with different content (`*`). + - `.missing_on_dst.txt`: paths present in the checksum manifest but absent from the checked source (`-`). + - `.missing_on_src.txt`: paths present in the checked source but absent from the checksum manifest (`+`). + - `.error.txt`: paths that could not be read or hashed (`!`). +- `rclone/check_after//` + - `.combined.txt`: combined post-copy source-to-destination comparison status, one path per line. + - `.match.txt`: paths whose content matched between source and destination (`=`). + - `.differ.txt`: paths present on both sides but with different content (`*`). + - `.missing_on_dst.txt`: paths found in the source but absent from the destination (`-`). + - `.missing_on_src.txt`: paths found at the destination but absent from the source (`+`). + - `.error.txt`: paths that could not be read or hashed (`!`). + +
    - +Two integrity stages create reports: -## Pipeline overview +1. **Pre-copy checksum validation** uses each supplied MD5 and/or SHA-256 manifest to check the source and publishes reports under `rclone/checksum_before//`. +2. **Post-copy validation** compares the source with the destination after the copy task finishes and publishes reports under `rclone/check_after//`. -The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: +Both stages use the same `.*.txt` naming convention and publish to `rclone/`. When a row supplies a checksum manifest, similarly named pre-copy and post-copy files may target the same published path; use the consolidated MultiQC sections for the stage-specific summary and retain the Nextflow work directory if both raw report sets must be audited independently. -- [FastQC](#fastqc) - Raw read QC -- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline -- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +The combined files use `rclone`'s one-character status prefixes: -### FastQC +| Prefix | Meaning | Action | +| ------ | ------------------------ | --------------------------------------------------------------------------------------------------------------------------- | +| `=` | File matches | No action required. | +| `-` | Missing from destination | Investigate an incomplete source checksum set or transfer. | +| `+` | Missing from source | Review unexpected destination content. The post-copy check uses `--one-way`, so destination-only files are tolerated there. | +| `*` | Content differs | Re-copy or investigate source/destination mutation. | +| `!` | Read/hash error | Inspect permissions, credentials, connectivity, and the copy log. | + +Empty category files mean that `rclone` reported no entries in that category. The commands are designed to preserve these reports rather than terminate the whole workflow on comparison differences. Always inspect the reports; workflow success alone is not an integrity guarantee. + +## MultiQC
    Output files -- `fastqc/` - - `*_fastqc.html`: FastQC report containing quality metrics. - - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. +- `multiqc/` + - `multiqc_report.html`: standalone report viewable in a browser. + - `multiqc_data/`: machine-readable data, logs, source inventory, software versions, and parsed rclone tables.
    -[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). +The MultiQC report consolidates: -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) +- validation summary containing `rclone checksum` and `rclone check` exit codes; +- checksum validation status for MD5 and/or SHA-256 manifests generated from `rclone checksum`; +- post-copy source-to-destination validation status generated from `rclone check`; +- the validated samplesheet and workflow parameter summary; and +- pipeline and tool versions. -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) +### Validation summary -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) +This section summarises the exit codes reported by the `rclone checksum` and `rclone check` modules for each sample. Use this table to quickly identify if any errors occurred in the source integrity or post-transfer checks. A more detailed file-by-file breakdown is provided in the following sections. -:::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: +Exit codes are reported using their corresponding rclone descriptions to make it easier to identify and troubleshoot any validation problems. A full list of exit codes and their meanings can be found in the [rclone documentation](https://rclone.org/docs/#list-of-exit-codes). -### MultiQC +![nf-core/multiqc validation summary](images/datasync-multiqc-exit-code-table.png) -
    -Output files +### `rclone checksum` section (source integrity checks) -- `multiqc/` - - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - - `multiqc_plots/`: directory containing static images from the report in various formats. +The MD5 and SHA-256 input-validation sections show the results from [`rclone checksum`](https://rclone.org/commands/rclone_checksum/). Use these sections to confirm that each source file matched the checksum manifest supplied in `checksum_md5` and/or `checksum_sha` before copying. -
    +When a samplesheet `input` points to S3, `rclone checksum` can normally validate MD5 manifests from S3 object hashes, but S3 does not provide SHA-256 object hashes for rclone to read remotely. SHA-256 validation for S3 inputs therefore requires the `--download` pipeline parameter to be enabled, which allows `rclone checksum` to download object data and calculate the hash locally during validation. + +![nf-core/multiqc checksum md5](images/datasync-multiqc-checksum-md5.png) -[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. +### `rclone check` section (post-transfer checks) -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . +The source-destination validation section shows the results from `rclone check` after the copy step. Use this section to confirm that copied files at `output_path` match the corresponding source files. -### Pipeline information +![nf-core/multiqc checksum md5](images/datasync-multiqc-post-transfer-check.png) + +Open `multiqc_report.html` after every run and investigate any non-matching, missing, or error entries. In the `rclone` result sections, entries are prioritised so rows needing attention are shown before successful matches: errors, mismatches, and missing-file statuses appear ahead of matching files. Data under `multiqc_data/` can be retained for automated auditing or downstream reporting; exact filenames may vary with the MultiQC version and the checksum types present in the samplesheet. + +## Pipeline information
    Output files - `pipeline_info/` - - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. - - Parameters used by the pipeline run: `params.json`. + - `nf_core_datasync_software_mqc_versions.yml`: versions of the pipeline and tools collected for MultiQC. + - `execution_timeline_.html`: chronological task execution view. + - `execution_report_.html`: task runtime and resource report. + - `execution_trace_.txt`: tabular task-level execution trace. + - `pipeline_dag_.html`: workflow dependency graph. + - Completion reports generated when `--email` or `--email_on_fail` is configured may also be present.
    -[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. +These files provide operational provenance and help diagnose performance or failures. Archive them with the MultiQC and rclone reports. The Nextflow `work/` directory and `.nextflow.log` remain in the launch directory rather than `--outdir`; keep them until transfer verification is complete if detailed troubleshooting or `-resume` may be needed. + +The supplied rclone configuration is an input credential file and is not intentionally copied to `--outdir`. Nevertheless, execution logs may contain remote names and object paths. Review logs before sharing them, and manage `rclone.conf` separately as a secret. + +[Nextflow](https://docs.seqera.io/platform-cloud/reports/overview) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. diff --git a/docs/usage.md b/docs/usage.md index 234441a..8966c72 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -2,65 +2,197 @@ ## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/datasync/usage](https://nf-co.re/datasync/usage) -> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ +> Pipeline parameter documentation is generated automatically from [`nextflow_schema.json`](../nextflow_schema.json). This page explains how to prepare a transfer and operate the pipeline. -## Introduction +## Prerequisites - +Install Nextflow 25.10.4 or later and use a supported software profile. Docker or Singularity/Apptainer is recommended for reproducibility. Ensure that the account running Nextflow can read each source and checksum manifest and can write to every destination. + +For cloud or other authenticated rclone remotes, create an [rclone configuration](https://rclone.org/docs/) and pass it with `--rclone_config`. The configuration applies to remote **sources and destinations**. The pipeline has currently been tested for transfers between S3 buckets. Other rclone-supported layouts, such as Azure Blob Storage to S3 or transfers between S3-compatible providers, should be configured and validated against the upstream `rclone` documentation for each provider before use. ## Samplesheet input -You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. +Supply a comma-separated samplesheet with `--input`: ```bash ---input '[path to samplesheet file]' +--input /path/to/samplesheet.csv ``` -### Multiple runs of the same sample +Each row describes an independent transfer. The header names are fixed; columns may be in any order. -The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: +| Column | Required | Description | +| -------------- | ------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Yes | Unique identifier used in task labels and output report names. It must not contain whitespace. Use a unique value for each row to prevent published report files from colliding. | +| `input` | Yes | Source file or directory. Use a local path or object-storage URI such as `s3://bucket/prefix`. HTTP(S) URLs and rclone-specific `remote:path` syntax are not supported. Whitespace is not allowed. | +| `output_path` | Yes | Destination directory. Use a local path such as `/archive/runs` or an object-storage URI such as `s3://bucket/prefix`. HTTP(S) URLs and rclone-specific `remote:path` syntax are not supported. Whitespace is not allowed. | +| `checksum_md5` | One checksum column | Path or URL to an MD5 checksum manifest used to validate `input` before copying. The manifest format is described below. Leave empty when using SHA-256 only. | +| `checksum_sha` | One checksum column | Path or URL to a SHA-256 checksum manifest used to validate `input` before copying. The manifest format is described below. Leave empty when using MD5 only. | -```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz +HTTP(S) URLs are not currently supported for `input` or `output_path`. The pipeline validates checksum manifests before copying and verifies the copied content afterwards; HTTP checksum behavior is not yet defined and tested for this workflow. Download HTTP-hosted data locally before including it in a samplesheet. + +At least one checksum manifest is required on every row. If both are supplied, both validations run. Checksum files must use the format accepted by [`rclone checksum`](https://rclone.org/commands/rclone_checksum/): one checksum record per line with the hash value followed by two spaces and then the file path. Paths must be relative to the source root from the `input` column, not absolute paths. + +For a directory input, paths are relative to the directory named in the samplesheet. For example, if `input` is `/data/run_001` and it contains `/data/run_001/reads/sample_R1.fastq.gz`, the checksum manifest path must be `reads/sample_R1.fastq.gz`, not the absolute path. For a single-file input, the pipeline checks the manifest against the file's parent directory, so the manifest path must be the file name. For example, an `input` of `/data/reference.fa` requires a manifest entry ending in `reference.fa`. + +You can generate a correctly formatted MD5 manifest with `rclone md5sum`. Write the manifest outside the input directory so that it is not included among the files being hashed: + +```bash +rclone md5sum ./data/run_001 > ./data/checksums/run_001_md5.txt +rclone md5sum ./data/reference.fa > ./data/checksums/reference_md5.txt +``` + +For SHA-256, use `rclone hashsum SHA256`: + +```bash +rclone hashsum SHA256 ./data/run_001 > ./data/checksums/run_001_sha256.txt ``` -### Full samplesheet +For an object-storage source, use the corresponding configured rclone remote syntax when generating the manifest. For example, the samplesheet input `s3://bucket/prefix` corresponds to `s3:bucket/prefix` when the rclone configuration contains an `[s3]` remote: -The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below. +```bash +rclone md5sum --config ./secure/rclone.conf s3:bucket/prefix > run_001_md5.txt +``` + +Checksum manifests may use a `.tsv`, `.txt`, `.md5` or `.sha256` filename extension, but their contents are not tab-separated or comma-separated tables and must not include a header. Each record is plain text with the hash and path separated by exactly **two spaces**. The required fields are: -A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. +| Field | Required | Description | +| ----- | -------- | -------------------------------------------------------------------------------------------------------------- | +| Hash | Yes | MD5 hash for `checksum_md5` files or SHA-256 hash for `checksum_sha` files. | +| Path | Yes | Path relative to a directory `input`, or the file name (without parent directories) for a single-file `input`. | + +Example samplesheet: ```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz -CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz, -TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, +sample,input,output_path,checksum_md5,checksum_sha +run_001,/data/run_001,s3://archive/runs,/data/checksums/run_001_md5.tsv, +reference,/data/reference.fa,/data/references,,/data/checksums/reference_sha256.tsv +run_002,/data/run_002,s3://archive/runs,/data/checksums/run_002_md5.tsv,/data/checksums/run_002_sha256.tsv ``` -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +For the `run_001` directory example, `/data/checksums/run_001_md5.tsv` could contain: + +```text title="run_001_md5.tsv" +d41d8cd98f00b204e9800998ecf8427e reads/sample_R1.fastq.gz +0cc175b9c0f1b6a831c399e269772661 reads/sample_R2.fastq.gz +900150983cd24fb0d6963f7d28e17f72 reports/qc_summary.txt +``` + +For a SHA-256 manifest, the same relative paths are used with SHA-256 hashes: + +```text title="run_001_sha256.tsv" +e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 reads/sample_R1.fastq.gz +ca978112ca1bbdcafac231b39a23dc4da786eff8147c4e72b9807785afee48bb reads/sample_R2.fastq.gz +ba7816bf8f01cfea414140de5dae2223b00361a396177a9cb410ff61f20015ad reports/qc_summary.txt +``` + +An [example samplesheet](../assets/samplesheet.csv) is included in the repository. + +## Configuring `rclone` remotes + +The file supplied with `--rclone_config` uses `rclone`'s INI-style format. + +Each `[name]` section defines an rclone remote used internally by the pipeline. Samplesheet paths must use local paths or standard URIs such as `s3://bucket/path`; `name:path` values are not accepted. For an `s3://` URI, configure the matching `[s3]` remote in the rclone configuration. + +> [!NOTE] +> The pipeline's documented and tested configuration pattern is S3-to-S3 transfer. + +One file may contain several sections for different providers, but samplesheet URIs select the remote that has the matching scheme name. Provider-specific options should be taken from the relevant `rclone` documentation. + +Create the file interactively where possible: + +```bash +rclone config --config /secure/rclone.conf +rclone listremotes --config /secure/rclone.conf +``` + +Then provide that exact file to the pipeline: + +```bash +nextflow run nf-core/datasync \ + -profile docker \ + --input samplesheet.csv \ + --outdir results \ + --rclone_config /secure/rclone.conf +``` + +### S3 and S3-compatible storage + +The main use case tested for nf-core/datasync is transferring files between S3 buckets. An S3 remote specifies the provider, region, and credentials. For example: + +```ini title="rclone.conf" +[s3] +type = s3 +provider = AWS +access_key_id = YOUR_ACCESS_KEY_ID +secret_access_key = YOUR_SECRET_ACCESS_KEY +region = eu-central-1 +``` + +Use `s3://bucket/path` for S3 sources and destinations in the samplesheet. The pipeline converts this to rclone's internal `s3:bucket/path` form, so ensure rclone has credentials and provider settings for the `[s3]` remote. Provider-specific settings vary: consult the [`rclone` S3 documentation](https://rclone.org/s3/) and your storage provider's endpoint, region, addressing-style, and credential documentation rather than copying example values unchanged. + +Because samplesheet paths use URI schemes rather than rclone remote names, a single samplesheet cannot select multiple differently configured S3 remotes. Use one `[s3]` configuration for the run, or run separate transfers when providers require different rclone configurations. + +## SHA256 checksum verification for remote inputs + +When validating files stored on cloud storage providers (e.g. S3, azure, google cloud), only MD5 hashes are typically available through the storage provider (see [Overview of cloud storage systems](https://rclone.org/overview/)). SHA256 checksums are not exposed by the remote API, so they cannot be verified directly. + +In order to validate SHA256 checksums for remote inputs, `rclone checksum` must download each file and compute its SHA256 checksum locally. If a `checksum_sha` file is provided for remote inputs, the `--download` parameter must be enabled. Otherwise, SHA checksum verification cannot be performed and the pipeline will terminate with an error. -An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. +> [!NOTE] +> Providing `--download` does not force all files to be downloaded in all modules. It is only used when verifying SHA256 checksum files for remote source directories in `RCLONE_CHECKSUM`. + +> [!WARNING] +> Enabling `--download` may incur substantial cloud data transfer and egress costs, particularly when validating large datasets. Make sure this is the intended behaviour before running the pipeline. + +## Copying only successfully validated files + +By default, the pipeline will copy all files in the source directory, regardless of whether they were successfully validated against the provided checksum or not. + +However, it is possible to restrict copying of files to only the ones that successfully pass checksum validation by enabling the `--copy_matching_only` parameter: + +- If only an MD5 checksum file is provided, only files that successfully match their MD5 checksum will be copied. +- If only a SHA256 checksum file is provided, only files that successfully match their SHA256 checksum will be copied. +- If both MD5 and SHA256 checksum files are provided, the pipeline will copy only files that successfully pass **both** checksum validations. + +Files that fail checksum validation, are missing, or cannot be verified are excluded from the copy operation when this parameter is enabled. + +## Destination layout + +The pipeline preserves the source basename: + +- for a file source, `rclone` copies the file into `output_path`, and validation expects `output_path/`; +- for a directory source, the pipeline appends the source directory name, so `/data/run_001` with `output_path=/archive/runs` is copied and checked at `/archive/runs/run_001`. + +A trailing slash on `output_path` is removed before these paths are constructed. Ensure that a destination does not already contain unrelated files: post-copy validation uses `rclone check --one-way`, which checks that source content exists and matches at the destination while tolerating destination-only files. You can override this behavior by providing your own config file with external arguments for `rclone check`. ## Running the pipeline -The typical command for running the pipeline is as follows: +A typical local-to-cloud run is: ```bash -nextflow run nf-core/datasync --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker +nextflow run nf-core/datasync \ + -r \ + -profile docker \ + --input ./data/samplesheet.csv \ + --outdir ./data/datasync-results \ + --rclone_config ./secure/rclone.conf ``` -This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. +`--outdir` stores logs, integrity reports, MultiQC, and execution metadata. It does **not** override the transfer destinations in the samplesheet. + +To inspect the proposed copy without writing destination data: + +```bash +nextflow run nf-core/datasync \ + -r \ + -profile docker \ + --input ./data/samplesheet.csv \ + --outdir ./data/datasync-dry-run \ + --rclone_config ./secure/rclone.conf \ + --rclone_dry_run +``` + +The checksum and post-copy check stages still run during a dry run. Consequently, post-copy results reflect whatever was already present at the destination rather than a simulated final state. Note that the pipeline will create the following files in your working directory: @@ -75,9 +207,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: +> [!WARNING] +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -85,9 +216,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/datasync -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' @@ -96,33 +227,116 @@ genome: 'GRCh37' You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). -### Updating the pipeline +### Real copy example + +The `test_copy` profile provides a small real-transfer example that can be used to test the pipeline locally. It copies public test directories to `results/destination`and verifies the copied files: + +```bash +nextflow run nf-core/datasync \ + -r \ + -profile test_copy,docker \ + --outdir ./data/datasync-test-copy-results +``` + +This profile does not use `--rclone_dry_run`; it transfers data to your local environment. Although the data is small, the run accesses cloud-hosted data and may incur network or cloud egress charges. Review your environment's costs before running this test profile. + +### Parameter files -When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: +Frequently reused settings can be stored in YAML or JSON and loaded with `-params-file`: + +```yaml title="params.yaml" +input: /data/samplesheet.csv +outdir: /data/datasync-results +rclone_config: /secure/rclone.conf +multiqc_title: July archive transfer +``` ```bash -nextflow pull nf-core/datasync +nextflow run nf-core/datasync -r -profile docker -params-file params.yaml +``` + +Do not use `-c` for pipeline parameters. Use it only for Nextflow executor, resources, and other infrastructure configuration. + +### Common integrity outcomes + +The workflow is designed to collect `rclone` reports even when `rclone` detects differences. The table below summarises common edge cases and how to interpret them in the published reports and MultiQC. + +| Situation | Where it is detected | Report status | Pipeline behaviour and action | +| ------------------------------------------------------------------ | ---------------------------------------------------------------- | --------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- | +| File exists and checksum/content matches | `rclone checksum` before copy and `rclone check` after copy | `=` / `Match` | Expected result; no action needed. | +| File is listed in the checksum manifest but absent from the source | Pre-copy `rclone checksum` | `-` / missing from checked source | The report is retained for review. Fix the manifest or restore the missing source file before relying on the transfer. | +| Source file exists but is absent from the checksum manifest | Pre-copy `rclone checksum` | `+` / missing from manifest | Review whether the manifest is incomplete or whether the extra source file should be excluded from the transfer. | +| Source file hash differs from the supplied manifest | Pre-copy `rclone checksum` | `*` / mismatch | Investigate source mutation, stale manifests, or incorrect checksum files before accepting the copy. | +| Source file cannot be read or hashed | Pre-copy `rclone checksum` | `!` / error | Inspect credentials, permissions, connectivity, and source path spelling. | +| Destination is missing a copied file | Post-copy `rclone check` | `-` / missing from destination | Treat as an incomplete transfer unless the file was intentionally excluded; re-run or inspect the rclone copy log. | +| Destination file exists but content differs from source | Post-copy `rclone check` | `*` / mismatch | Re-copy or investigate concurrent source/destination changes. | +| Destination contains files absent from the source | Post-copy `rclone check` | `+` / missing from source | The post-copy check uses `--one-way`, so destination-only files are tolerated, but should still be reviewed for unexpected stale or unrelated data. | +| Dry-run execution | Copy step uses `--dry-run`; checksum and check reports still run | Depends on existing destination | No transfer data is written. Post-copy reports describe whatever was already present at the destination. | + +### Including or excluding files + +Filter files by passing additional `rclone` filter flags to the relevant rclone module through a Nextflow configuration file. `rclone` supports flags such as `--include`, `--exclude`, `--filter`, `--files-from`, and related rule files; see the [`rclone` filtering documentation](https://rclone.org/filtering/) for rule syntax and ordering. + +For example, to copy and check only FASTQ files while excluding temporary files, create a small infrastructure config: + +```groovy title="rclone_filters.config" +process { + withName: 'RCLONE_COPY' { + ext.args = { + [ + '--log-level INFO', + '--stats 30s', + '--stats-one-line', + '--stats-log-level INFO', + '--s3-chunk-size 64M', + '--no-check-certificate', + params.rclone_dry_run ? '--dry-run' : '', + '--include "*.fastq.gz"', + '--include "*.fq.gz"', + '--exclude "*.tmp"', + '--exclude "*"' + ].findAll { it }.join(' ') + } + } + + withName: 'RCLONE_CHECK' { + ext.args = { + [ + '--no-check-certificate', + '--one-way', + '--include "*.fastq.gz"', + '--include "*.fq.gz"', + '--exclude "*.tmp"', + '--exclude "*"' + ].join(' ') + } + } +} ``` +Run it with `-c rclone_filters.config` in addition to your normal profile and parameters. Because `ext.args` overrides module defaults, include the default `rclone` flags you still need when adding filters. Keep checksum manifests consistent with the same filtering rules: if a file is intentionally excluded from copy/check, remove it from the checksum manifest or generate a manifest for only the included files. + +## Understanding completion and integrity + +For each row, the pipeline first validates supplied checksum manifests, performs the copy, and then compares source and destination. `rclone` comparison commands write status reports even when differences are found, allowing all results to be collected in MultiQC. Therefore, a successful Nextflow run means the workflow completed; it does **not by itself** prove every object matched. Review `multiqc/multiqc_report.html` and the reports under `rclone/`, especially lines marked `-`, `+`, `*`, or `!` (see [output documentation](output.md)). + ### Reproducibility -It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. +It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. First, go to the [nf-core/datasync releases page](https://github.com/nf-core/datasync/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. +To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: +> [!TIP] +> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. ## Core Nextflow arguments -:::note -These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). -::: +> [!NOTE] +> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen) ### `-profile` @@ -130,16 +344,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -:::info -We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -::: +> [!IMPORTANT] +> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment. - `test` - A profile with a complete configuration for automated testing @@ -153,9 +366,11 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `shifter` - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) + - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) +- `wave` + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. @@ -173,21 +388,32 @@ Specify the path to a specific config file (this is a core Nextflow command). Se ### Resource requests -Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. +The `rclone` processes use the `process_low` label. Configure executors and override CPU, memory, or time in a Nextflow config, for example: + +```groovy title="resources.config" +process { + withLabel: process_low { + cpus = 8 + memory = '16 GB' + time = '12h' + } +} +``` -To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. +Run with `-c resources.config`. `rclone` derives its checker count from allocated CPUs, and the copy step uses roughly half that count (minimum one) for parallel transfers. +To change the resource requests, please see the [max resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#set-max-resources) and [customise process resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-resources) section of the nf-core website. ### Custom Containers -In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. +In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. -To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#update-tool-versions) section of the nf-core website. ### Custom Tool Arguments A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#modifying-tool-arguments) section of the nf-core website. ### nf-core/configs @@ -196,29 +422,3 @@ In most cases, you will only need to create a custom config as a one-off but if See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files. If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). - -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - -## Running in the background - -Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. - -The Nextflow `-bg` flag launches Nextflow in the background, detached from your terminal so that the workflow does not stop if you log out of your session. The logs are saved to a file. - -Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time. -Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs). - -## Nextflow memory requirements - -In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. -We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`): - -```bash -NXF_OPTS='-Xms1g -Xmx4g' -``` diff --git a/main.nf b/main.nf index e0833f6..d62052e 100644 --- a/main.nf +++ b/main.nf @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -21,19 +19,6 @@ include { DATASYNC } from './workflows/datasync' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_datasync_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_datasync_pipeline' -include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_datasync_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// TODO nf-core: Remove this line if you don't need a FASTA file -// This is an example of how to use getGenomeAttribute() to fetch parameters -// from igenomes.config using `--genome` -params.fasta = getGenomeAttribute('fasta') - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -54,12 +39,15 @@ workflow NFCORE_DATASYNC { // WORKFLOW: Run pipeline // DATASYNC ( - samplesheet + samplesheet, + params.multiqc_config, + params.multiqc_logo, + params.multiqc_methods_description, + params.outdir, + params.rclone_config ) - emit: multiqc_report = DATASYNC.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -70,18 +58,19 @@ workflow NFCORE_DATASYNC { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, params.outdir, - params.input + params.input, + params.help, + params.help_full, + params.show_hidden ) // @@ -90,7 +79,6 @@ workflow { NFCORE_DATASYNC ( PIPELINE_INITIALISATION.out.samplesheet ) - // // SUBWORKFLOW: Run completion tasks // @@ -100,7 +88,6 @@ workflow { params.plaintext_email, params.outdir, params.monochrome_logs, - params.hook_url, NFCORE_DATASYNC.out.multiqc_report ) } diff --git a/modules.json b/modules.json index 028ff6d..ef4f2b6 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,22 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", + "installed_by": ["modules"] + }, + "rclone/check": { + "branch": "master", + "git_sha": "0f1a09cd10bb7a05bfedb3d8780f985751f9c614", + "installed_by": ["modules"] + }, + "rclone/checksum": { + "branch": "master", + "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686", + "installed_by": ["modules"] + }, + "rclone/copy": { + "branch": "master", + "git_sha": "0f1a09cd10bb7a05bfedb3d8780f985751f9c614", "installed_by": ["modules"] } } @@ -16,17 +31,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436", "installed_by": ["subworkflows"] } } diff --git a/modules/local/create_filter_list/main.nf b/modules/local/create_filter_list/main.nf new file mode 100644 index 0000000..1da22b7 --- /dev/null +++ b/modules/local/create_filter_list/main.nf @@ -0,0 +1,13 @@ +process CREATE_FILTER_LIST { + tag "$meta.id" + + input: + tuple val(meta), val(common) + + output: + tuple val(meta), path('files_to_copy.txt') + + exec: + def outFile = task.workDir.resolve('files_to_copy.txt') + outFile.text = common.join('\n') + '\n' +} diff --git a/modules/local/sync/sync.nf b/modules/local/sync/sync.nf deleted file mode 100644 index f7d8e0b..0000000 --- a/modules/local/sync/sync.nf +++ /dev/null @@ -1,40 +0,0 @@ -process SYNC { - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3'}" - - input: - tuple val(run_id), path(origin), path(sync) // [run_id, rundir, origin] - - output: //We do not really have outputs, this happens in the directories already as they are just "mounted" and copied over from - tuple val(run_id), path(${run_id}_sha256_checksums.txt) , emit: synced - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in pipelines/archivetmcp/bin/ - """ - //Run checksums first - for file in $(find ${origin} -type f) - do - sha256sum ${file} >> ${run_id}_sha256_checksums.txt - touch ${origin}/CHECKSUM_DONE ##Needs to be parameterized , currently always creates this - done - fi - - //Run actual sync step - rsync -crptgo ${origin} ${sync} - - //Touch SYNC DONE - touch ${origin}/SYNC_DONE - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt new file mode 100644 index 0000000..2a91c22 --- /dev/null +++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt @@ -0,0 +1,1526 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/bioconda/ +options: +pypi-prerelease-mode: if-necessary-or-explicit +packages: +linux-64: +- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda +- conda: 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+timestamp: 1764777111296 diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt new file mode 100644 index 0000000..a55a4d4 --- /dev/null +++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt @@ -0,0 +1,126 @@ + +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885 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+https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda#5b5203189eb668f042ac2b0826244964 +https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda#e941e85e273121222580723010bd4fa2 +https://conda.anaconda.org/conda-forge/noarch/packaging-26.1-pyhc364b38_0.conda#b8ae38639d323d808da535fb71e31be8 +https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda#cea962410e327262346d48d01f05936c +https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda#f731af71c723065d91b4c01bb822641b +https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda#87d58d103b47c4a8567b3d7666647684 +https://conda.anaconda.org/conda-forge/noarch/narwhals-2.20.0-pyhcf101f3_0.conda#6cac1a50359219d786453c6fef819f98 +https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda#3e9427ee186846052e81fadde8ebe96a +https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.0-py310hff09b76_0.conda#d5628a33ce7652511e38fc98643dc910 +https://conda.anaconda.org/conda-forge/noarch/polars-1.40.0-pyh58ad624_0.conda#fd16be490f5403adfbf27dd4901bbe34 +https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.40.0-py310hf00a4a2_0.conda#a82af0fcbb72db253dc89a7a45279372 +https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda#ef0340e75068ac8ff96462749b5c98e7 +https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda#032d8030e4a24fe1f72c74423a46fb88 +https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda#9ae2c92975118058bd720e9ba2bb7c58 +https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda#e17be1016bcc3516827b836cd3e4d9dc +https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.3-py314h451b6cc_0.conda#1a2cb55be9a153ad6203bff6b787c240 +https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6 +https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98 +https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c +https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2 +https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac +https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130 +https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59 +https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0 +https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66 +https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9 +https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a +https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864 +https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6 +https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206 +https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b +https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873 +https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f +https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 2212096..7a970e2 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,7 @@ -name: multiqc +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.20 + - bioconda::multiqc=1.35 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 354f443..c4bc715 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,55 +1,50 @@ process MULTIQC { + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : - 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' + : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" input: - path multiqc_files, stageAs: "?/*" - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) + tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions + tuple val(meta), path("*.html"), emit: report + tuple val(meta), path("*_data"), emit: data + tuple val(meta), path("*_plots"), emit: plots, optional: true + // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever + tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' + def config = multiqc_config ? multiqc_config instanceof List ? "--config ${multiqc_config.join(' --config ')}" : "--config ${multiqc_config}" : "" + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ - $args \\ - $config \\ - $extra_config \\ - $logo \\ + ${args} \\ + ${config} \\ + ${prefix} \\ + ${logo} \\ + ${replace} \\ + ${samples} \\ . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ stub: """ mkdir multiqc_data - touch multiqc_plots + touch multiqc_data/.stub + mkdir multiqc_plots + touch multiqc_plots/.stub touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ } diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc3..27ce18d 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples + into a single report keywords: - QC - bioinformatics tools @@ -11,41 +12,91 @@ tools: It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] + licence: + - "GPL-3.0-or-later" + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + ontologies: [] + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + ontologies: [] + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 + - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 output: - - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*.html": + type: file + description: MultiQC report file + pattern: ".html" + ontologies: [] + data: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + plots: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_plots" + ontologies: [] + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - multiqc: + type: string + description: The tool name + - multiqc --version | sed "s/.* //g": + type: eval + description: The expression to obtain the version of the tool authors: - "@abhi18av" - "@bunop" @@ -56,3 +107,27 @@ maintainers: - "@bunop" - "@drpatelh" - "@jfy133" +containers: + conda: + linux/amd64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt + linux/arm64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt + docker: + linux/amd64: + name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc + build_id: bd-c17fb751507e9dfc_1 + scan_id: sc-3b1b3932f9846892_1 + linux/arm64: + name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5 + build_id: bd-5c84a5000a226ab5_1 + scan_id: sc-0d39df41e9737bbd_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2 + build_id: bd-c680f2aea25ccec2_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data + linux/arm64: + name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81 + build_id: bd-c0468833d65b2f81_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data diff --git a/modules/nf-core/multiqc/tests/custom_prefix.config b/modules/nf-core/multiqc/tests/custom_prefix.config new file mode 100644 index 0000000..b30b135 --- /dev/null +++ b/modules/nf-core/multiqc/tests/custom_prefix.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = "custom_prefix" + } +} diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242..4cbdb95 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,28 +8,91 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } + } + test("sarscov2 single-end [fastqc] - custom prefix") { + config "./custom_prefix.config" + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) + """ + } + } + + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } } test("sarscov2 single-end [fastqc] [config]") { @@ -37,21 +100,85 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) - input[2] = [] - input[3] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } + } + + test("sarscov2 single-end [fastqc] [multiple configs]") { + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [ + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true) + ], + [], + [], + [] + ]) + """ + } + } + + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -62,23 +189,23 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.report.collect { file(it).getName() } + - process.out.data.collect { file(it).getName() } + - process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index c204b48..4489921 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,41 +1,422 @@ { - "multiqc_versions_single": { + "sarscov2 single-end [fastqc] [multiple configs]": { "content": [ - [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } ], + "timestamp": "2026-03-17T16:15:42.577775492", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-14T09:28:51.744211298" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_stub": { + "sarscov2 single-end [fastqc]": { "content": [ - [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } ], + "timestamp": "2026-03-17T16:21:17.072841555", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-14T09:29:28.847433492" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_versions_config": { + "sarscov2 single-end [fastqc] - stub": { "content": [ - [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" - ] + { + "data": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "plots": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "report": [ + [ + { + "id": "FASTQC" + }, + "multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } ], + "timestamp": "2026-02-26T15:14:39.789193051", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-14T09:29:13.223621555" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] [config]": { + "content": [ + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } + ], + "timestamp": "2026-03-17T16:15:30.372239611", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] - custom prefix": { + "content": [ + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "custom_prefix.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } + ], + "timestamp": "2026-03-17T16:15:18.189023981", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 0000000..374dfef --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + ext.args = '-p' + } +} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d..0000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/modules/nf-core/rclone/check/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt b/modules/nf-core/rclone/check/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt new file mode 100644 index 0000000..d9222c8 --- /dev/null +++ b/modules/nf-core/rclone/check/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt @@ -0,0 +1,81 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/conda-forge/ +options: +pypi-prerelease-mode: if-necessary-or-explicit +packages: +linux-64: +- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/rclone-1.74.3-h519d9b9_0.conda +packages: +- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda +build_number: 20 +sha256: 1dd3fffd892081df9726d7eb7e0dea6198962ba775bd88842135a4ddb4deb3c9 +md5: a9f577daf3de00bca7c3c76c0ecbd1de +depends: +- __glibc >=2.17,<3.0.a0 +- libgomp >=7.5.0 +constrains: +- openmp_impl <0.0a0 +license: BSD-3-Clause +license_family: BSD +size: 28948 +timestamp: 1770939786096 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda +sha256: 8e0a3b5e41272e5678499b5dfc4cddb673f9e935de01eb0767ce857001229f46 +md5: 57736f29cc2b0ec0b6c2952d3f101b6a +depends: +- __glibc >=2.17,<3.0.a0 +- _openmp_mutex >=4.5 +constrains: +- libgcc-ng ==15.2.0=*_19 +- libgomp 15.2.0 he0feb66_19 +license: GPL-3.0-only WITH GCC-exception-3.1 +license_family: GPL +size: 1041084 +timestamp: 1778269013026 +- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda +sha256: 5abe4ab9d93f6c9757d654f1969ae2267d4505315c1f2f8fe705fd60af084f1b +md5: faac990cb7aedc7f3a2224f2c9b0c26c +depends: +- __glibc >=2.17,<3.0.a0 +license: GPL-3.0-only WITH GCC-exception-3.1 +license_family: GPL +size: 603817 +timestamp: 1778268942614 +- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda +sha256: fc89f74bbe362fb29fa3c037697a89bec140b346a2469a90f7936d1d7ea4d8a3 +md5: fc21868a1a5aacc937e7a18747acb8a5 +depends: +- __glibc >=2.17,<3.0.a0 +- libgcc >=14 +license: X11 AND BSD-3-Clause +size: 918956 +timestamp: 1777422145199 +- conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda +sha256: 4ce2e1ee31a6217998f78c31ce7dc0a3e0557d9238b51d49dd20c52d467a126d +md5: f2c23a77b25efcad57d377b34bd84941 +depends: +- __glibc >=2.17,<3.0.a0 +- libgcc >=14 +- ncurses >=6.5,<7.0a0 +license: GPL-2.0-or-later AND LGPL-2.0-or-later +license_family: GPL +size: 593603 +timestamp: 1769710381284 +- conda: https://conda.anaconda.org/conda-forge/linux-64/rclone-1.74.3-h519d9b9_0.conda +sha256: 74a49ffb12e8c974519e856e5cb19d2a3c0aa9538847fa616149a4e7576a8106 +md5: df1b9c8554e9fdb3e7610cde037b0757 +license: MIT +license_family: MIT +size: 45039813 +timestamp: 1780709814295 diff --git a/modules/nf-core/rclone/check/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt b/modules/nf-core/rclone/check/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt new file mode 100644 index 0000000..d8994c6 --- /dev/null +++ b/modules/nf-core/rclone/check/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt @@ -0,0 +1,75 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/conda-forge/ +options: 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X11 AND BSD-3-Clause +size: 960036 +timestamp: 1777422174534 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda +sha256: e9cbcbc94e151ada3d6dc365380aaaf591f65012c16d9a2abaea4b9b90adc402 +md5: ab7288cc39545556d1bc5e71ab2df9a9 +depends: +- libgcc >=14 +- ncurses >=6.5,<7.0a0 +license: GPL-2.0-or-later AND LGPL-2.0-or-later +license_family: GPL +size: 636733 +timestamp: 1769712412683 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/rclone-1.74.3-h8f1e559_0.conda +sha256: 6aef9a68af8b200db69a915073ba2285e01e95e363626921497074588fbd8493 +md5: d63c4d8337e3a0128716f6f515a1ed05 +license: MIT +license_family: MIT +size: 41497679 +timestamp: 1780709811705 diff --git a/modules/nf-core/rclone/check/environment.yml b/modules/nf-core/rclone/check/environment.yml new file mode 100644 index 0000000..ea96315 --- /dev/null +++ b/modules/nf-core/rclone/check/environment.yml @@ -0,0 +1,6 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge +dependencies: + - "conda-forge::rclone=1.74.3" diff --git a/modules/nf-core/rclone/check/main.nf b/modules/nf-core/rclone/check/main.nf new file mode 100644 index 0000000..e913b29 --- /dev/null +++ b/modules/nf-core/rclone/check/main.nf @@ -0,0 +1,94 @@ +process RCLONE_CHECK { + tag "${meta.id}" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data' + : 'community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97' }" + + input: + tuple val(meta), val(source), val(destination) + path rclone_config + + output: + tuple val(meta), path("${prefix}.combined.txt") , emit: combined , optional: true + tuple val(meta), path("${prefix}.differ.txt") , emit: differ , optional: true + tuple val(meta), path("${prefix}.missing_on_dst.txt") , emit: missing_on_dst, optional: true + tuple val(meta), path("${prefix}.missing_on_src.txt") , emit: missing_on_src, optional: true + tuple val(meta), path("${prefix}.match.txt") , emit: match , optional: true + tuple val(meta), path("${prefix}.error.txt") , emit: error , optional: true + tuple val(meta), path("${prefix}.exit_code.txt") , emit: exit_code , optional: true + tuple val("${task.process}"), val('rclone'), eval("rclone --version | sed -n '1s/^rclone v//p'"), topic: versions, emit: versions_rclone + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def configArg = rclone_config ? "--config ${rclone_config}" : '' + + def sourceString = source.toString() + def normalizedSource = sourceString.replaceFirst('^([a-zA-Z][a-zA-Z0-9+.-]*)://', '$1:') + def sourceHttpUrlArg = '' + + if (sourceString ==~ /^https?:\/\/.*/) { + def sourceMatcher = (sourceString =~ /^(https?:\/\/[^\/]+)(\/.*)?$/) + if (!sourceMatcher.matches()) { + throw new IllegalArgumentException("Invalid HTTP(S) source '${sourceString}' for sample '${meta.id}'.") + } + sourceHttpUrlArg = "--http-url '${sourceMatcher[0][1]}'" + normalizedSource = ":http:${(sourceMatcher[0][2] ?: '/').replaceFirst('^/', '')}" + } + + """ + touch \\ + ${prefix}.combined.txt \\ + ${prefix}.differ.txt \\ + ${prefix}.missing_on_dst.txt \\ + ${prefix}.missing_on_src.txt \\ + ${prefix}.match.txt \\ + ${prefix}.error.txt + + rclone check ${configArg} \\ + ${sourceHttpUrlArg} \\ + $args \\ + --combined ${prefix}.combined.txt \\ + --differ ${prefix}.differ.txt \\ + --missing-on-dst ${prefix}.missing_on_dst.txt \\ + --missing-on-src ${prefix}.missing_on_src.txt \\ + --match ${prefix}.match.txt \\ + --error ${prefix}.error.txt \\ + --checkers $task.cpus \\ + "${normalizedSource}" \\ + ${destination} \\ + && echo 0 > ${prefix}.exit_code.txt \\ + || echo \$? > ${prefix}.exit_code.txt + + sort -k2 ${prefix}.combined.txt -o ${prefix}.combined.txt + sort ${prefix}.differ.txt -o ${prefix}.differ.txt + sort ${prefix}.missing_on_dst.txt -o ${prefix}.missing_on_dst.txt + sort ${prefix}.missing_on_src.txt -o ${prefix}.missing_on_src.txt + sort ${prefix}.match.txt -o ${prefix}.match.txt + sort ${prefix}.error.txt -o ${prefix}.error.txt + + # Do not emit empty output files + for f in *.txt; do + [ -s "\$f" ] || rm -f "\$f" + done + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch \\ + ${prefix}.combined.txt \\ + ${prefix}.differ.txt \\ + ${prefix}.missing_on_dst.txt \\ + ${prefix}.missing_on_src.txt \\ + ${prefix}.match.txt \\ + ${prefix}.error.txt + """ +} diff --git a/modules/nf-core/rclone/check/meta.yml b/modules/nf-core/rclone/check/meta.yml new file mode 100644 index 0000000..2ae5d92 --- /dev/null +++ b/modules/nf-core/rclone/check/meta.yml @@ -0,0 +1,180 @@ +name: "rclone_check" +description: Check that files in source and destination paths match +keywords: + - check + - checksum + - cloud + - sync +tools: + - "rclone": + description: "Rclone is a command-line program to manage files on cloud storage." + homepage: "https://rclone.org/" + documentation: "https://rclone.org/commands/rclone_check/" + tool_dev_url: "https://github.com/rclone/rclone" + licence: + - "MIT" + +input: + - - meta: + type: map + description: | + Groovy Map containing source information + e.g. [ id:'test' ] + - source: + type: string + description: | + File or directory containing source files to compare. This should be a path understood by Rclone, + such as a local path or a configured remote path. + Examples: `data/input`, `s3:bucket/path`, `gs:bucket/path`, + `remote:path/to/data`. + - destination: + type: string + description: | + Directory containing destination files to compare. This should be the fully resolved target + path understood by Rclone, such as a local path or a configured remote + path. The module does not append sample IDs, basenames, or modify this + path internally. + Examples: `results/output`, `s3:bucket/output`, `gs:bucket/output`, + `remote:path/to/output`. + - rclone_config: + type: file + description: | + Rclone configuration file defining the remotes used by source_path and/or + destination_path. Authentication and remote-specific options should be + configured in this file where possible. + pattern: "*.conf" + ontologies: [] +output: + combined: + - - meta: + type: map + description: | + Groovy Map containing source information + e.g. [ id:'test' ] + - ${prefix}.combined.txt: + type: file + description: Combined report of matching, missing, differing, and error paths. + pattern: "*.combined.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + differ: + - - meta: + type: map + description: | + Groovy Map containing source information + e.g. [ id:'test' ] + - ${prefix}.differ.txt: + type: file + description: Report of paths present in both source and destination but different. + pattern: "*.differ.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + missing_on_dst: + - - meta: + type: map + description: | + Groovy Map containing source information + e.g. [ id:'test' ] + - ${prefix}.missing_on_dst.txt: + type: file + description: Report of paths present in source but missing from destination. + pattern: "*.missing_on_dst.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + missing_on_src: + - - meta: + type: map + description: | + Groovy Map containing source information + e.g. [ id:'test' ] + - ${prefix}.missing_on_src.txt: + type: file + description: Report of paths present in destination but missing from source. + pattern: "*.missing_on_src.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + match: + - - meta: + type: map + description: | + Groovy Map containing source information + e.g. [ id:'test' ] + - ${prefix}.match.txt: + type: file + description: Report of matching paths. + pattern: "*.match.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + error: + - - meta: + type: map + description: | + Groovy Map containing source information + e.g. [ id:'test' ] + - ${prefix}.error.txt: + type: file + description: Report of paths with read or hash errors. + pattern: "*.error.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + exit_code: + - - meta: + type: map + description: | + Groovy Map containing checksum source information + e.g. [ id:'test' ] + - ${prefix}.exit_code.txt: + type: file + description: File with exit status. + pattern: "*.exit_code.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + versions_rclone: + - - ${task.process}: + type: string + description: The name of the process + - rclone: + type: string + description: The name of the tool + - rclone --version | sed -n '1s/^rclone v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - rclone: + type: string + description: The name of the tool + - rclone --version | sed -n '1s/^rclone v//p': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@atrigila" +maintainers: + - "@atrigila" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/rclone:1.74.3--351f8e39202b129a + build_id: bd-351f8e39202b129a_1 + scan_id: sc-0e6358c70409ff39_1 + linux/amd64: + name: community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97 + build_id: bd-2ef33c5b9132aa97_1 + scan_id: sc-2cbce8a89ac463aa_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/rclone:1.74.3--af6486c6ac506f82 + build_id: bd-af6486c6ac506f82_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data + linux/arm64: + name: oras://community.wave.seqera.io/library/rclone:1.74.3--49a53709aa05d28d + build_id: bd-49a53709aa05d28d_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/de/de06d232599f015aa253f63b84ba2e257bb542810dc11714b88ca9b4045b80ea/data + conda: + linux/amd64: + lock_file: modules/nf-core/rclone/check/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt + linux/arm64: + lock_file: modules/nf-core/rclone/check/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt diff --git a/modules/nf-core/rclone/check/tests/main.nf.test b/modules/nf-core/rclone/check/tests/main.nf.test new file mode 100644 index 0000000..88d545f --- /dev/null +++ b/modules/nf-core/rclone/check/tests/main.nf.test @@ -0,0 +1,92 @@ +nextflow_process { + + name "Test Process RCLONE_CHECK" + script "../main.nf" + process "RCLONE_CHECK" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "rclone" + tag "rclone/check" + + test("match - malt") { + when { + process { + """ + file('rclone.config').text = '[s3]\\ntype = s3\\nprovider = AWS\\nregion = eu-west-1\\nenv_auth = false\\nno_check_bucket = true' + + input[0] = [[id:'test'], "s3://nf-core-test-datasets/modules/data/delete_me/malt/", "s3://nf-core-test-datasets/modules/data/delete_me/malt/"] + input[1] = file('rclone.config') + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("sarscov2 - fastq - stub") { + options "-stub" + + when { + process { + """ + input[0] = [[id:'test'], params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/', params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/'] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("different files") { + when { + process { + """ + file('rclone.config').text = '[https]\\ntype = http\\n[s3]\\ntype = s3\\nprovider = AWS\\nregion = eu-west-1\\nenv_auth = false\\nno_check_bucket = true' + + input[0] = [[id:'test'], "s3://nf-core-test-datasets/modules/data/delete_me/malt/", "s3://annotation-cache/snpeff_cache/WBcel235.105/"] + input[1] = file('rclone.config') + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("differ and missing") { + when { + process { + """ + file('rclone.config').text = '[https]\\ntype = http\\n[s3]\\ntype = s3\\nprovider = AWS\\nregion = eu-west-1\\nenv_auth = false\\nno_check_bucket = true' + + input[0] = [[id:'test'], "s3://nf-core-test-datasets/modules/data/delete_me/mirtop/", "s3://nf-core-test-datasets/modules/data/delete_me/metabuli"] + input[1] = file('rclone.config') + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } +} diff --git a/modules/nf-core/rclone/check/tests/main.nf.test.snap b/modules/nf-core/rclone/check/tests/main.nf.test.snap new file mode 100644 index 0000000..423a41f --- /dev/null +++ b/modules/nf-core/rclone/check/tests/main.nf.test.snap @@ -0,0 +1,248 @@ +{ + "match - malt": { + "content": [ + { + "combined": [ + [ + { + "id": "test" + }, + "test.combined.txt:md5,6518ec1170e94cd1e9d2ef4a4ba5a9e8" + ] + ], + "differ": [ + + ], + "error": [ + + ], + "exit_code": [ + [ + { + "id": "test" + }, + "test.exit_code.txt:md5,897316929176464ebc9ad085f31e7284" + ] + ], + "match": [ + [ + { + "id": "test" + }, + "test.match.txt:md5,66c7833b0fd04a059b29a116474c021c" + ] + ], + "missing_on_dst": [ + + ], + "missing_on_src": [ + + ], + "versions_rclone": [ + [ + "RCLONE_CHECK", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-09-02T19:03:10.104368524", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "sarscov2 - fastq - stub": { + "content": [ + { + "combined": [ + [ + { + "id": "test" + }, + "test.combined.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "differ": [ + [ + { + "id": "test" + }, + "test.differ.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "error": [ + [ + { + "id": "test" + }, + "test.error.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "exit_code": [ + + ], + "match": [ + [ + { + "id": "test" + }, + "test.match.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "missing_on_dst": [ + [ + { + "id": "test" + }, + "test.missing_on_dst.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "missing_on_src": [ + [ + { + "id": "test" + }, + "test.missing_on_src.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_rclone": [ + [ + "RCLONE_CHECK", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-08-04T11:26:42.333790108", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "different files": { + "content": [ + { + "combined": [ + [ + { + "id": "test" + }, + "test.combined.txt:md5,750454d95092af361bdb1c3e8c113251" + ] + ], + "differ": [ + + ], + "error": [ + + ], + "exit_code": [ + [ + { + "id": "test" + }, + "test.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1" + ] + ], + "match": [ + + ], + "missing_on_dst": [ + [ + { + "id": "test" + }, + "test.missing_on_dst.txt:md5,66c7833b0fd04a059b29a116474c021c" + ] + ], + "missing_on_src": [ + [ + { + "id": "test" + }, + "test.missing_on_src.txt:md5,1dd18b615ae0c9abf940ad0739fb8950" + ] + ], + "versions_rclone": [ + [ + "RCLONE_CHECK", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-08-04T11:26:48.79499383", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "differ and missing": { + "content": [ + { + "combined": [ + [ + { + "id": "test" + }, + "test.combined.txt:md5,74c774156fdfa62f1ba14c780adf89f4" + ] + ], + "differ": [ + [ + { + "id": "test" + }, + "test.differ.txt:md5,ac036608c5c402f92926505d0f0ab0e4" + ] + ], + "error": [ + + ], + "exit_code": [ + [ + { + "id": "test" + }, + "test.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1" + ] + ], + "match": [ + + ], + "missing_on_dst": [ + [ + { + "id": "test" + }, + "test.missing_on_dst.txt:md5,6435d60effdac7ca6fbdfad40ffe2535" + ] + ], + "missing_on_src": [ + [ + { + "id": "test" + }, + "test.missing_on_src.txt:md5,89fcd615fd22b904204dafd407daf015" + ] + ], + "versions_rclone": [ + [ + "RCLONE_CHECK", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-08-04T11:26:55.797148658", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/rclone/check/tests/nextflow.config b/modules/nf-core/rclone/check/tests/nextflow.config new file mode 100644 index 0000000..b208cef --- /dev/null +++ b/modules/nf-core/rclone/check/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + withName: 'RCLONE_CHECK' { + ext.args = { + "--no-check-certificate" + } + } +} diff --git a/modules/nf-core/rclone/checksum/environment.yml b/modules/nf-core/rclone/checksum/environment.yml new file mode 100644 index 0000000..ea96315 --- /dev/null +++ b/modules/nf-core/rclone/checksum/environment.yml @@ -0,0 +1,6 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge +dependencies: + - "conda-forge::rclone=1.74.3" diff --git a/modules/nf-core/rclone/checksum/main.nf b/modules/nf-core/rclone/checksum/main.nf new file mode 100644 index 0000000..3b43e5e --- /dev/null +++ b/modules/nf-core/rclone/checksum/main.nf @@ -0,0 +1,96 @@ +process RCLONE_CHECKSUM { + tag "${meta.id}" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data' + : 'community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97' }" + + input: + tuple val(meta), path(sumfile), val(hash), val(destination) + path rclone_config + + output: + tuple val(meta), path("${prefix}.combined.txt") , emit: combined , optional: true + tuple val(meta), path("${prefix}.differ.txt") , emit: differ , optional: true + tuple val(meta), path("${prefix}.missing_on_dst.txt") , emit: missing_on_dst, optional: true + tuple val(meta), path("${prefix}.missing_on_src.txt") , emit: missing_on_src, optional: true + tuple val(meta), path("${prefix}.match.txt") , emit: match , optional: true + tuple val(meta), path("${prefix}.error.txt") , emit: error , optional: true + tuple val(meta), path("${prefix}.exit_code.txt") , emit: exit_code , optional: true + tuple val("${task.process}"), val('rclone'), eval("rclone --version | sed -n '1s/^rclone v//p'"), topic: versions, emit: versions_rclone + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def configArg = rclone_config ? "--config ${rclone_config}" : '' + + def destinationString = destination.toString() + def normalizedDestination = destinationString.replaceFirst('^([a-zA-Z][a-zA-Z0-9+.-]*)://', '$1:') + def destinationHttpUrlArg = '' + + if (destinationString ==~ /^https?:\/\/.*/) { + def destinationMatcher = (destinationString =~ /^(https?:\/\/[^\/]+)(\/.*)?$/) + if (!destinationMatcher.matches()) { + throw new IllegalArgumentException("Invalid HTTP(S) destination '${destinationString}' for sample '${meta.id}'.") + } + destinationHttpUrlArg = "--http-url '${destinationMatcher[0][1]}'" + normalizedDestination = ":http:${(destinationMatcher[0][2] ?: '/').replaceFirst('^/', '')}" + } + + """ + touch \\ + ${prefix}.combined.txt \\ + ${prefix}.differ.txt \\ + ${prefix}.missing_on_dst.txt \\ + ${prefix}.missing_on_src.txt \\ + ${prefix}.match.txt \\ + ${prefix}.error.txt + + rclone checksum ${configArg} \\ + --copy-links \\ + ${destinationHttpUrlArg} \\ + $args \\ + --combined ${prefix}.combined.txt \\ + --differ ${prefix}.differ.txt \\ + --missing-on-dst ${prefix}.missing_on_dst.txt \\ + --missing-on-src ${prefix}.missing_on_src.txt \\ + --match ${prefix}.match.txt \\ + --error ${prefix}.error.txt \\ + --checkers $task.cpus \\ + $hash \\ + $sumfile \\ + "${normalizedDestination}" \\ + && echo 0 > ${prefix}.exit_code.txt \\ + || echo \$? > ${prefix}.exit_code.txt + + sort -k2 ${prefix}.combined.txt -o ${prefix}.combined.txt + sort ${prefix}.differ.txt -o ${prefix}.differ.txt + sort ${prefix}.missing_on_dst.txt -o ${prefix}.missing_on_dst.txt + sort ${prefix}.missing_on_src.txt -o ${prefix}.missing_on_src.txt + sort ${prefix}.match.txt -o ${prefix}.match.txt + sort ${prefix}.error.txt -o ${prefix}.error.txt + + # Do not emit empty output files + for f in *.txt; do + [ -s "\$f" ] || rm -f "\$f" + done + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch \\ + ${prefix}.combined.txt \\ + ${prefix}.differ.txt \\ + ${prefix}.missing_on_dst.txt \\ + ${prefix}.missing_on_src.txt \\ + ${prefix}.match.txt \\ + ${prefix}.error.txt + """ +} diff --git a/modules/nf-core/rclone/checksum/meta.yml b/modules/nf-core/rclone/checksum/meta.yml new file mode 100644 index 0000000..bec4f79 --- /dev/null +++ b/modules/nf-core/rclone/checksum/meta.yml @@ -0,0 +1,188 @@ +name: "rclone_checksum" +description: Check files in a destination path against a checksum SUM file +keywords: + - checksum + - md5 + - sha1 + - cloud + - sync +tools: + - "rclone": + description: "Rclone is a command-line program to manage files on cloud storage." + homepage: "https://rclone.org/" + documentation: "https://rclone.org/commands/rclone_checksum/" + tool_dev_url: "https://github.com/rclone/rclone" + licence: + - "MIT" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing checksum source information + e.g. [ id:'test' ] + - sumfile: + type: file + description: Checksum SUM file containing hashes and destination paths to + verify. + pattern: "*.{md5,sha1,sha256,sum,txt}" + ontologies: + - edam: "http://edamontology.org/data_3671" + - hash: + type: string + description: Hash type to check, for example MD5, SHA1, or SHA256. + - destination: + type: string + description: | + Directory containing destination files to check against the SUM file. This should be the fully resolved target + path understood by Rclone, such as a local path or a configured remote + path. The module does not append sample IDs, basenames, or modify this + path internally. + Examples: `results/output`, `s3:bucket/output`, `gs:bucket/output`, + `remote:path/to/output`. + - rclone_config: + type: file + description: | + Rclone configuration file defining the remotes used by source_path and/or + destination_path. Authentication and remote-specific options should be + configured in this file where possible. + pattern: "*.conf" + ontologies: [] +output: + combined: + - - meta: + type: map + description: | + Groovy Map containing checksum source information + e.g. [ id:'test' ] + - ${prefix}.combined.txt: + type: file + description: Combined report of matching, missing, differing, and error + paths. + pattern: "*.combined.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + differ: + - - meta: + type: map + description: | + Groovy Map containing checksum source information + e.g. [ id:'test' ] + - ${prefix}.differ.txt: + type: file + description: Report of paths present in both source SUM file and + destination but different. + pattern: "*.differ.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + missing_on_dst: + - - meta: + type: map + description: | + Groovy Map containing checksum source information + e.g. [ id:'test' ] + - ${prefix}.missing_on_dst.txt: + type: file + description: Report of paths present in the SUM file but missing from + the destination. + pattern: "*.missing_on_dst.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + missing_on_src: + - - meta: + type: map + description: | + Groovy Map containing checksum source information + e.g. [ id:'test' ] + - ${prefix}.missing_on_src.txt: + type: file + description: Report of paths present in the destination but missing from + the SUM file. + pattern: "*.missing_on_src.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + match: + - - meta: + type: map + description: | + Groovy Map containing checksum source information + e.g. [ id:'test' ] + - ${prefix}.match.txt: + type: file + description: Report of matching paths. + pattern: "*.match.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + error: + - - meta: + type: map + description: | + Groovy Map containing checksum source information + e.g. [ id:'test' ] + - ${prefix}.error.txt: + type: file + description: Report of paths with read or hash errors. + pattern: "*.error.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + exit_code: + - - meta: + type: map + description: | + Groovy Map containing checksum source information + e.g. [ id:'test' ] + - ${prefix}.exit_code.txt: + type: file + description: File with exit status. + pattern: "*.exit_code.txt" + ontologies: + - edam: "http://edamontology.org/data_3671" + versions_rclone: + - - ${task.process}: + type: string + description: The name of the process + - rclone: + type: string + description: The name of the tool + - rclone --version | sed -n '1s/^rclone v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - rclone: + type: string + description: The name of the tool + - rclone --version | sed -n '1s/^rclone v//p': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@atrigila" +maintainers: + - "@atrigila" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/rclone:1.74.3--351f8e39202b129a + build_id: bd-351f8e39202b129a_1 + scan_id: sc-0e6358c70409ff39_1 + linux/amd64: + name: community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97 + build_id: bd-2ef33c5b9132aa97_1 + scan_id: sc-2cbce8a89ac463aa_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/rclone:1.74.3--af6486c6ac506f82 + build_id: bd-af6486c6ac506f82_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data + linux/arm64: + name: oras://community.wave.seqera.io/library/rclone:1.74.3--49a53709aa05d28d + build_id: bd-49a53709aa05d28d_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/de/de06d232599f015aa253f63b84ba2e257bb542810dc11714b88ca9b4045b80ea/data + conda: + linux/amd64: + lock_file: modules/nf-core/rclone/checksum/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt + linux/arm64: + lock_file: modules/nf-core/rclone/checksum/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt diff --git a/modules/nf-core/rclone/checksum/tests/main.nf.test b/modules/nf-core/rclone/checksum/tests/main.nf.test new file mode 100644 index 0000000..746d594 --- /dev/null +++ b/modules/nf-core/rclone/checksum/tests/main.nf.test @@ -0,0 +1,76 @@ +nextflow_process { + + name "Test Process RCLONE_CHECKSUM" + script "../main.nf" + process "RCLONE_CHECKSUM" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "rclone" + tag "rclone/checksum" + + test("test - md5 - match") { + + when { + process { + """ + file('rclone.config').text = '[s3]\\ntype = s3\\nprovider = AWS\\nregion = eu-west-1\\nenv_auth = false\\nno_check_bucket = true' + + input[0] = [[id:'test'], file(params.modules_testdata_base_path + 'generic/txt/snpeff_cache_md5.txt', checkIfExists: true), 'MD5', "s3://annotation-cache/snpeff_cache/WBcel235.105/"] + input[1] = file('rclone.config') + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test - md5 - stub") { + options "-stub" + + when { + process { + """ + file('test.md5').text = 'e59ff97941044f85df5297e1c302d260 hello.txt\\n' + + input[0] = [[id:'test'], file('test.md5'), 'MD5', "s3://nf-core-test-datasets/modules/data/delete_me/malt/"] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test - md5 - differs") { + when { + process { + """ + file('test_bad.md5').text = '00000000000000000000000000000000 hello.txt' + file('rclone.config').text = '[s3]\\ntype = s3\\nprovider = AWS\\nregion = eu-west-1\\nenv_auth = false\\nno_check_bucket = true' + + input[0] = [[id:'test'], file('test_bad.md5'), 'MD5', "s3://annotation-cache/snpeff_cache/WBcel235.105/"] + input[1] = file('rclone.config') + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } +} diff --git a/modules/nf-core/rclone/checksum/tests/main.nf.test.snap b/modules/nf-core/rclone/checksum/tests/main.nf.test.snap new file mode 100644 index 0000000..f0d6ace --- /dev/null +++ b/modules/nf-core/rclone/checksum/tests/main.nf.test.snap @@ -0,0 +1,179 @@ +{ + "test - md5 - match": { + "content": [ + { + "combined": [ + [ + { + "id": "test" + }, + "test.combined.txt:md5,4b849f0b6831d6561da709ca6f626b7d" + ] + ], + "differ": [ + + ], + "error": [ + + ], + "exit_code": [ + [ + { + "id": "test" + }, + "test.exit_code.txt:md5,897316929176464ebc9ad085f31e7284" + ] + ], + "match": [ + [ + { + "id": "test" + }, + "test.match.txt:md5,2458aa282a426dec085359d209d5077c" + ] + ], + "missing_on_dst": [ + + ], + "missing_on_src": [ + + ], + "versions_rclone": [ + [ + "RCLONE_CHECKSUM", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-09-02T19:03:42.461174852", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "test - md5 - differs": { + "content": [ + { + "combined": [ + [ + { + "id": "test" + }, + "test.combined.txt:md5,d79adc0e541e01c95735769c919ae993" + ] + ], + "differ": [ + + ], + "error": [ + + ], + "exit_code": [ + [ + { + "id": "test" + }, + "test.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1" + ] + ], + "match": [ + + ], + "missing_on_dst": [ + [ + { + "id": "test" + }, + "test.missing_on_dst.txt:md5,a438474115db37daf9d8e1307c06eb4a" + ] + ], + "missing_on_src": [ + + ], + "versions_rclone": [ + [ + "RCLONE_CHECKSUM", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-08-04T11:27:20.066820454", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "test - md5 - stub": { + "content": [ + { + "combined": [ + [ + { + "id": "test" + }, + "test.combined.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "differ": [ + [ + { + "id": "test" + }, + "test.differ.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "error": [ + [ + { + "id": "test" + }, + "test.error.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "exit_code": [ + + ], + "match": [ + [ + { + "id": "test" + }, + "test.match.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "missing_on_dst": [ + [ + { + "id": "test" + }, + "test.missing_on_dst.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "missing_on_src": [ + [ + { + "id": "test" + }, + "test.missing_on_src.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_rclone": [ + [ + "RCLONE_CHECKSUM", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-08-04T11:27:14.250267458", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/rclone/checksum/tests/nextflow.config b/modules/nf-core/rclone/checksum/tests/nextflow.config new file mode 100644 index 0000000..a78067e --- /dev/null +++ b/modules/nf-core/rclone/checksum/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + withName: 'RCLONE_CHECKSUM' { + ext.args = { + "--no-check-certificate --one-way" + } + } +} diff --git a/modules/nf-core/rclone/copy/environment.yml b/modules/nf-core/rclone/copy/environment.yml new file mode 100644 index 0000000..ea96315 --- /dev/null +++ b/modules/nf-core/rclone/copy/environment.yml @@ -0,0 +1,6 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge +dependencies: + - "conda-forge::rclone=1.74.3" diff --git a/modules/nf-core/rclone/copy/main.nf b/modules/nf-core/rclone/copy/main.nf new file mode 100644 index 0000000..fb99e85 --- /dev/null +++ b/modules/nf-core/rclone/copy/main.nf @@ -0,0 +1,58 @@ +process RCLONE_COPY { + tag "${meta.id}" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data' + : 'community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97' }" + + input: + tuple val(meta), val(source_path), val(destination_path), path(filter_file) + path rclone_config + + output: + tuple val(meta), path("*rclone-copy.log"), emit: log + tuple val("${task.process}"), val('rclone'), eval("rclone --version | sed -n '1s/^rclone v//p'"), topic: versions, emit: versions_rclone + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def configArg = rclone_config ? "--config '${rclone_config}'" : '' + def transfers = Math.max(1, task.cpus.intdiv(2)) + def checkers = task.cpus + + // Handle HTTP URLs: split into --http-url base and :http:relative_path + def source_string = source_path.toString() + def rclone_source + def http_url_arg = '' + + if (source_string ==~ /^https?:\/\/.*/) { + def matcher = (source_string =~ /^(https?:\/\/[^\/]+)(\/.*)?$/) + if (!matcher.matches()) { + throw new IllegalArgumentException("Invalid HTTP(S) source '${source_string}' for sample '${meta.id}'.") + } + http_url_arg = "--http-url '${matcher[0][1]}'" + rclone_source = ":http:${(matcher[0][2] ?: '/').replaceFirst('^/', '')}" + } else { + rclone_source = source_string.replaceFirst('^([a-zA-Z][a-zA-Z0-9+.-]*)://', '$1:') + } + + """ + rclone ${configArg} copy \\ + ${http_url_arg} \\ + ${args} \\ + --log-file "${meta.id}-rclone-copy.log" \\ + --transfers ${transfers} \\ + --checkers ${checkers} \\ + "${rclone_source}" \\ + "${destination_path}" + """ + + stub: + """ + touch rclone-copy.log + """ +} diff --git a/modules/nf-core/rclone/copy/meta.yml b/modules/nf-core/rclone/copy/meta.yml new file mode 100644 index 0000000..18c5bf1 --- /dev/null +++ b/modules/nf-core/rclone/copy/meta.yml @@ -0,0 +1,116 @@ +name: "rclone_copy" +description: Copy files or directories between local and/or remote storage using Rclone +keywords: + - rclone + - copy + - sync + - data-transfer +tools: + - "rclone": + description: "Rclone is a command line program to manage files on cloud storage" + homepage: "https://rclone.org/" + documentation: "https://rclone.org/docs/" + licence: + - "MIT" + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - source_path: + type: string + description: | + Source path to copy from. This should be a path understood by Rclone, + such as a local path or a configured remote path. + Examples: `data/input`, `s3:bucket/path`, `gs:bucket/path`, + `remote:path/to/data`. + - destination_path: + type: string + description: | + Destination path to copy to. This should be the fully resolved target + path understood by Rclone, such as a local path or a configured remote + path. The module does not append sample IDs, basenames, or modify this + path internally. + Examples: `results/output`, `s3:bucket/output`, `gs:bucket/output`, + `remote:path/to/output`. + - filter_file: + type: file + description: | + Optional plain text file containing one file path or pattern per line to be + passed to Rclone copy as a filter list (e.g. via `--files-from` or + `--include-from`). This input is only used when the corresponding rclone + filtering option is enabled through the module configuration. + - rclone_config: + type: file + description: | + Rclone configuration file defining the remotes used by source_path and/or + destination_path. Authentication and remote-specific options should be + configured in this file where possible. + pattern: "*.conf" + ontologies: [] +output: + log: + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - "*rclone-copy.log": + type: file + description: Rclone log file generated during the copy operation. + pattern: "*rclone-copy.log" + ontologies: [] + versions_rclone: + - - ${task.process}: + type: string + description: The name of the process + - rclone: + type: string + description: The name of the tool + - rclone --version | sed -n '1s/^rclone v//p': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - rclone: + type: string + description: The name of the tool + - rclone --version | sed -n '1s/^rclone v//p': + type: eval + description: The expression to obtain the version of the tool + +authors: + - "@antoniasaracco" +maintainers: + - "@antoniasaracco" +containers: + docker: + linux/amd64: + name: community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be + build_id: bd-ff88b2e0040147be_1 + scan_id: sc-ff88b2e0040147be_1 + linux/arm64: + name: community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be + build_id: bd-ff88b2e0040147be_1 + scan_id: sc-ff88b2e0040147be_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be + build_id: bd-ff88b2e0040147be_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c947c1a7171daf074310295417d0f0afe879275e1543fa5fc2a9711e7c2c72ab/data + linux/arm64: + name: oras://community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be + build_id: bd-ff88b2e0040147be_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c947c1a7171daf074310295417d0f0afe879275e1543fa5fc2a9711e7c2c72ab/data + conda: + linux/amd64: + lock_file: modules/nf-core/rclone/copy/.conda-lock/linux_amd64-bd-ff88b2e0040147be_1.txt + linux/arm64: + lock_file: modules/nf-core/rclone/copy/.conda-lock/linux_arm64-bd-ff88b2e0040147be_1.txt diff --git a/modules/nf-core/rclone/copy/tests/main.nf.test b/modules/nf-core/rclone/copy/tests/main.nf.test new file mode 100644 index 0000000..85d92a0 --- /dev/null +++ b/modules/nf-core/rclone/copy/tests/main.nf.test @@ -0,0 +1,97 @@ +nextflow_process { + + name "Test RCLONE_COPY" + script "../main.nf" + process "RCLONE_COPY" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "rclone" + tag "rclone/copy" + + test("homo_sapiens - gvcf - copy from https - dry-run") { + + when { + params { + exclude_from = false + } + process { + """ + input[0] = [ + [ id:'test' ], + params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', + '/tmp/', + [] + ] + input[1] = [] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log"])).match() } + ) + } + } + + test("homo_sapiens - gvcf - filter - dry-run") { + + when { + params { + exclude_from = true + } + process { + """ + file('exclude.txt').text = 'test.genome.vcf.gz' + + input[0] = [ + [ id:'test' ], + params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', + '/tmp/', + file('exclude.txt') + ] + input[1] = [] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log"])).match() } + ) + } + } + + test("homo_sapiens - gvcf - copy from https - stub") { + + options "-stub" + + when { + params { + exclude_from = true + } + process { + """ + input[0] = [ + [ id:'test' ], + params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', + '/tmp/', + [] + ] + input[1] = [] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } +} diff --git a/modules/nf-core/rclone/copy/tests/main.nf.test.snap b/modules/nf-core/rclone/copy/tests/main.nf.test.snap new file mode 100644 index 0000000..d23bb7d --- /dev/null +++ b/modules/nf-core/rclone/copy/tests/main.nf.test.snap @@ -0,0 +1,80 @@ +{ + "homo_sapiens - gvcf - copy from https - stub": { + "content": [ + { + "log": [ + [ + { + "id": "test" + }, + "rclone-copy.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_rclone": [ + [ + "RCLONE_COPY", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-09-02T19:04:23.232858558", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo_sapiens - gvcf - copy from https - dry-run": { + "content": [ + { + "log": [ + [ + { + "id": "test" + }, + "test-rclone-copy.log" + ] + ], + "versions_rclone": [ + [ + "RCLONE_COPY", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-09-02T19:04:05.861448709", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "homo_sapiens - gvcf - filter - dry-run": { + "content": [ + { + "log": [ + [ + { + "id": "test" + }, + "test-rclone-copy.log" + ] + ], + "versions_rclone": [ + [ + "RCLONE_COPY", + "rclone", + "1.74.3-DEV" + ] + ] + } + ], + "timestamp": "2026-09-02T19:04:13.800329186", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/rclone/copy/tests/nextflow.config b/modules/nf-core/rclone/copy/tests/nextflow.config new file mode 100644 index 0000000..dd7038e --- /dev/null +++ b/modules/nf-core/rclone/copy/tests/nextflow.config @@ -0,0 +1,14 @@ +process { + withName: 'RCLONE_COPY' { + ext.args = { + def base_args = [ + '--dry-run', + '--no-check-certificate' + ] + if (params.exclude_from) { + base_args.add("--exclude-from ${filter_file}") + } + base_args.join(' ') + } + } +} diff --git a/nextflow.config b/nextflow.config index 7b66a17..a2e4e93 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,186 +9,192 @@ // Global default params, used in configs params { - // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - // References - genome = null - igenomes_base = 's3://ngi-igenomes/igenomes/' - igenomes_ignore = false - fasta = null// MultiQC options + + // MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null max_multiqc_email_size = '25.MB' multiqc_methods_description = null + // Rclone options + rclone_config = null + rclone_dry_run = false + copy_matching_only = false + download = false + // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - version = false + outdir = null + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + help = false + help_full = false + show_hidden = false + version = false + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/datasync/' + trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') // Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true } +// Backwards compatibility for publishDir syntax +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode + // Load base.config by default for all pipelines includeConfig 'conf/base.config' +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/datasync custom profiles from different institutions. -// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! -// try { -// includeConfig "${params.custom_config_base}/pipeline/datasync.config" -// } catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/datasync profiles: ${params.custom_config_base}/pipeline/datasync.config") -// } profiles { debug { - dumpHashes = true - process.beforeScript = 'echo $HOSTNAME' - cleanup = false + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false nextflow.enable.configProcessNamesValidation = true } conda { - conda.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - channels = ['conda-forge', 'bioconda', 'defaults'] - apptainer.enabled = false + conda.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + conda.channels = ['conda-forge', 'bioconda'] + apptainer.enabled = false } mamba { - conda.enabled = true - conda.useMamba = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + conda.enabled = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } docker { - docker.enabled = true - conda.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + docker.enabled = true + conda.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' + } + arm64 { + process.arch = 'arm64' + // See https://github.com/nf-core/modules/issues/6694 + // For now if you're using arm64 you have to use wave for the sake of the maintainers + // wave profile + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' } - arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + emulate_amd64 { + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { - singularity.enabled = true - singularity.autoMounts = true - conda.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + singularity.enabled = true + singularity.autoMounts = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } podman { - podman.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + podman.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } shifter { - shifter.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + shifter.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } charliecloud { - charliecloud.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - apptainer.enabled = false + charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + apptainer.enabled = false } apptainer { - apptainer.enabled = true - apptainer.autoMounts = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + apptainer.enabled = true + apptainer.autoMounts = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } - gitpod { - executor.name = 'local' - executor.cpus = 4 - executor.memory = 8.GB + wave { + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } + gpu { + docker.runOptions = '-u $(id -u):$(id -g) --gpus all' + apptainer.runOptions = '--nv' + singularity.runOptions = '--nv' } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } + test_copy { includeConfig 'conf/test_copy.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +// Load nf-core custom profiles from different institutions -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} +// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. +// Load nf-core/datasync custom profiles from different institutions. +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" + + +// Load nf-core/datasync custom profiles from nf-core/configs when available. +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/datasync.config" : "/dev/null" + +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' -// Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -200,73 +206,102 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = [ + "bash", + "-C", // No clobber - prevent output redirection from overwriting files. + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o", // Returns the status of the last command to exit.. + "pipefail" // ..with a non-zero status or zero if all successfully execute +] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false -def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html" } report { enabled = true - file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html" } trace { enabled = true - file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt" } dag { enabled = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html" } manifest { name = 'nf-core/datasync' - author = """Alexander Peltzer""" + contributors = [ + [ + name: 'Alexander Peltzer', + affiliation: '', + email: '', + github: '', + contribution: ['author'], + orcid: '' + ], + [ + name: 'Antonia Saracco', + affiliation: '', + email: '', + github: '', + contribution: ['contributor'], + orcid: '' + ], + [ + name: 'Delfina Terradas', + affiliation: '', + email: '', + github: '', + contribution: ['contributor'], + orcid: '' + ], + [ + name: 'Anabella Trigila', + affiliation: '', + email: '', + github: '', + contribution: ['contributor'], + orcid: '' + ], + [ + name: 'Julian Schwab', + affiliation: '', + email: '', + github: '', + contribution: ['author'], + orcid: '' + ], + [ + name: 'Gregor Sturm', + affiliation: '', + email: '', + github: '', + contribution: ['author'], + orcid: '' + ], + ] homePage = 'https://github.com/nf-core/datasync' description = """A simple sysops pipeline that can be used to synchronize, integrity check and permanently archive data.""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' - version = '1.0dev' + defaultBranch = 'main' + nextflowVersion = '!>=25.10.4' + version = '1.0.0' doi = '' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.7.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } - } +validation { + monochromeLogs = params.monochrome_logs } diff --git a/nextflow_schema.json b/nextflow_schema.json index dbf346f..a4a5f43 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/nf-core/datasync/master/nextflow_schema.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/nf-core/datasync/main/nextflow_schema.json", "title": "nf-core/datasync pipeline parameters", "description": "A simple sysops pipeline that can be used to synchronize, integrity check and permanently archive data.", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -40,37 +40,32 @@ "type": "string", "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", "fa_icon": "fas fa-file-signature" - } - } - }, - "reference_genome_options": { - "title": "Reference genome options", - "type": "object", - "fa_icon": "fas fa-dna", - "description": "Reference genome related files and options required for the workflow.", - "properties": { - "genome": { - "type": "string", - "description": "Name of iGenomes reference.", - "fa_icon": "fas fa-book", - "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details." }, - "fasta": { + "rclone_config": { "type": "string", "format": "file-path", "exists": true, - "mimetype": "text/plain", - "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", - "description": "Path to FASTA genome file.", - "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", - "fa_icon": "far fa-file-code" + "description": "Path to the rclone config file used for cloud storage authentication.", + "help_text": "Provide an rclone config file to support cloud providers such as AWS S3 or Azure Blob Storage. This file is loaded by rclone when copying data.", + "fa_icon": "fas fa-cog" }, - "igenomes_ignore": { + "rclone_dry_run": { "type": "boolean", - "description": "Do not load the iGenomes reference config.", - "fa_icon": "fas fa-ban", - "hidden": true, - "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + "description": "Perform a dry run of the rclone copy command.", + "fa_icon": "fas fa-forward", + "help_text": "If set, the pipeline will not actually copy any files to the destination. Instead, it will print out what would have been copied. This is useful for testing and debugging." + }, + "copy_matching_only": { + "type": "boolean", + "description": "Only copy files that matched their provided input checksums.", + "fa_icon": "fas fa-copy", + "help_text": "If set, the pipeline will only copy files that were correctly validated and will skip any file that did not match their input checksum." + }, + "download": { + "type": "boolean", + "description": "Download remote files for sha256 checksum verification in `RCLONE_CHECKSUM`.", + "fa_icon": "fas fa-cloud-download-alt", + "help_text": "If set, `RCLONE_CHECKSUM` will download remote files for any sample for which a SHA256 file was provided." } } }, @@ -122,41 +117,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -164,12 +124,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -213,13 +167,6 @@ "fa_icon": "fas fa-palette", "hidden": true }, - "hook_url": { - "type": "string", - "description": "Incoming hook URL for messaging service", - "fa_icon": "fas fa-people-group", - "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", - "hidden": true - }, "multiqc_config": { "type": "string", "format": "file-path", @@ -245,45 +192,43 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + "pipelines_testdata_base_path": { + "type": "string", + "fa_icon": "far fa-check-circle", + "description": "Base URL or local path to location of pipeline test dataset files", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/datasync/", + "hidden": true }, - "validationFailUnrecognisedParams": { + "trace_report_suffix": { + "type": "string", + "fa_icon": "far calendar", + "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", + "hidden": true + }, + "help": { + "type": ["boolean", "string"], + "description": "Display the help message." + }, + "help_full": { "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + "description": "Display the full detailed help message." }, - "validationLenientMode": { + "show_hidden": { "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." + "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)." } } } }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/reference_genome_options" - }, - { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 0000000..c0c14da --- /dev/null +++ b/nf-test.config @@ -0,0 +1,39 @@ +config { + // location for all nf-test tests + testsDir = "." + + // nf-test directory including temporary files for each test + workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" + + // location of an optional nextflow.config file specific for executing tests + configFile = "tests/nextflow.config" + + // ignore tests coming from the nf-core/modules repo + ignore = [ + 'modules/nf-core/**/tests/*', + 'subworkflows/nf-core/**/tests/*', + ] + + // run all test with defined profile(s) from the main nextflow.config + profile = "test" + + // list of filenames or patterns that should be trigger a full test run + triggers = [ + '.github/actions/nf-test/action.yml', + '.github/workflows/nf-test.yml', + 'assets/schema_input.json', + 'bin/*', + 'conf/test.config', + 'nextflow.config', + 'nextflow_schema.json', + 'nf-test.config', + 'tests/.nftignore', + 'tests/nextflow.config', + ] + + // load the necessary plugins + plugins { + load "nft-utils@0.0.3" + load "nft-csv@0.1.0" + } +} diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 5611062..0000000 --- a/pyproject.toml +++ /dev/null @@ -1,15 +0,0 @@ -# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff. -# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. -[tool.ruff] -line-length = 120 -target-version = "py38" -cache-dir = "~/.cache/ruff" - -[tool.ruff.lint] -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] - -[tool.ruff.lint.isort] -known-first-party = ["nf_core"] - -[tool.ruff.lint.per-file-ignores] -"__init__.py" = ["E402", "F401"] diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json new file mode 100644 index 0000000..919556e --- /dev/null +++ b/ro-crate-metadata.json @@ -0,0 +1,365 @@ +{ + "@context": [ + "https://w3id.org/ro/crate/1.2/context", + { + "GithubService": "https://w3id.org/ro/terms/test#GithubService", + "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", + "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine", + "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition", + "TestInstance": "https://w3id.org/ro/terms/test#TestInstance", + "TestService": "https://w3id.org/ro/terms/test#TestService", + "TestSuite": "https://w3id.org/ro/terms/test#TestSuite", + "TravisService": "https://w3id.org/ro/terms/test#TravisService", + "definition": "https://w3id.org/ro/terms/test#definition", + "engineVersion": "https://w3id.org/ro/terms/test#engineVersion", + "instance": "https://w3id.org/ro/terms/test#instance", + "resource": "https://w3id.org/ro/terms/test#resource", + "runsOn": "https://w3id.org/ro/terms/test#runsOn" + } + ], + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "creativeWorkStatus": "Stable", + "datePublished": "2026-09-08T15:38:46+00:00", + "description": "

    \n \n \n \"nf-core/datasync\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/datasync)\n[![GitHub Actions CI Status](https://github.com/nf-core/datasync/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/datasync/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/datasync/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/datasync/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/datasync/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/datasync)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23datasync-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/datasync)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/datasync** is a Nextflow pipeline for copying files and directories between storage locations and documenting their integrity. For every row in an input samplesheet, the pipeline:\n\n1. validates the source against a supplied MD5 and/or SHA-256 checksum manifest using [`rclone checksum`](https://rclone.org/commands/rclone_checksum/);\n2. copies the source to the requested destination with [`rclone copy`](https://rclone.org/);\n3. compares the copied data with the source using [`rclone check`](https://rclone.org/commands/rclone_check/); and\n4. produces detailed `rclone` status files and a consolidated MultiQC report.\n\nSources and destinations may be local paths or object-storage URIs such as Amazon S3, S3-compatible storage, or Azure Blob Storage. HTTP(S) URLs are not currently supported for samplesheet `input` or `output_path` values.\n\nThe current tested use case for this pipeline is transfer between S3 buckets.\n\nPass an `rclone` configuration with `--rclone_config` whenever a source or destination URI needs credentials or provider settings. Samplesheet paths use local paths or standard URIs such as `s3://bucket/path`, not rclone's `remote:path` syntax. For non-S3 layouts, design and validate the provider-specific configuration using the upstream [rclone documentation](https://rclone.org/docs/).\n\n![nf-core/datasync metro map](docs/images/datasync_nf-metro.svg)\n\n## Quick start\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, see the [nf-core environment setup guide](https://nf-co.re/docs/get_started/environment_setup/overview). Nextflow 25.10.4 or later is required.\n\nTo explore the pipeline outputs before preparing your own data, run the bundled `test` profile with a container profile:\n\n```bash\nnextflow run nf-core/datasync \\\n -profile test,docker \\\n --outdir results\n```\n\nThe `test` profile supplies a small samplesheet and `rclone` configuration automatically. It also enables `--rclone_dry_run`, so no files are actually transferred. This makes it useful for exploring the `rclone/` output folders and `multiqc/multiqc_report.html`; remember that post-copy comparison reports describe whatever is already present at the destination because the dry run does not write transfer data.\n\nTo run the pipeline on your own data, create a samplesheet containing one transfer per row:\n\n```csv\nsample,input,output_path,checksum_md5,checksum_sha\nrun_001,/data/run_001,s3://archive/runs,/data/manifests/run_001_md5.tsv\nreference,/data/reference.fa,/data/references,,/data/manifests/reference_sha256.tsv\n```\n\nThen launch the pipeline using:\n\n```bash\nnextflow run nf-core/datasync \\\n -r \\\n -profile docker \\\n --input samplesheet.csv \\\n --outdir results \\\n --rclone_config /path/to/rclone.conf\n```\n\n`--rclone_config` is optional only when every source and destination is accessible without a configured rclone remote. See the [`rclone` configuration section](docs/usage.md#configuring-rclone-remotes) for the tested S3-to-S3 use case and guidance on adapting rclone configuration files for other providers. To preview copy operations without transferring data, add `--rclone_dry_run`; note that subsequent comparison reports will then describe the unchanged destination.\n\nSee the [usage documentation](docs/usage.md) for samplesheet rules, destination semantics, remote configuration, and reproducible execution. The complete generated parameter reference is available on the [nf-core pipeline page](https://nf-co.re/datasync/parameters).\n\n## Pipeline output\n\nResults are written below `--outdir`. See the [output documentation](docs/output.md) for file names and status-code interpretation.\n\n## Credits\n\nnf-core/datasync was originally written by Alexander Peltzer.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Julian Schwab\n- Gregor Sturm\n- Antonia Saracco\n- Delfina Terradas\n- Anabella Trigila\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#datasync` channel](https://nfcore.slack.com/channels/datasync) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "hasPart": [ + { + "@id": "main.nf" + }, + { + "@id": "assets/" + }, + { + "@id": "bin/" + }, + { + "@id": "conf/" + }, + { + "@id": "docs/" + }, + { + "@id": "docs/images/" + }, + { + "@id": "modules/" + }, + { + "@id": "modules/nf-core/" + }, + { + "@id": "workflows/" + }, + { + "@id": "subworkflows/" + }, + { + "@id": "nextflow.config" + }, + { + "@id": "README.md" + }, + { + "@id": "nextflow_schema.json" + }, + { + "@id": "CHANGELOG.md" + }, + { + "@id": "LICENSE" + }, + { + "@id": "CODE_OF_CONDUCT.md" + }, + { + "@id": "CITATIONS.md" + }, + { + "@id": "modules.json" + }, + { + "@id": "docs/usage.md" + }, + { + "@id": "docs/output.md" + }, + { + "@id": ".nf-core.yml" + }, + { + "@id": ".pre-commit-config.yaml" + }, + { + "@id": ".prettierignore" + } + ], + "isBasedOn": "https://github.com/nf-core/datasync", + "license": "MIT", + "mainEntity": { + "@id": "main.nf" + }, + "mentions": [ + { + "@id": "#77ce8e20-3bfe-48e3-a2ef-1e81d74d71b6" + } + ], + "name": "nf-core/datasync" + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.2" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] + }, + { + "@id": "main.nf", + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], + "contributor": [ + { + "@id": "#be129ed0-c83e-444b-85dd-6db2c42dc277" + }, + { + "@id": "#b293152b-1358-4678-a5a5-8603ccb89cd0" + }, + { + "@id": "#6e1f504a-fae3-4fca-a7b7-8d84fff28bbd" + } + ], + "dateCreated": "", + "dateModified": "2026-09-08T15:38:46Z", + "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", + "keywords": [ + "nf-core", + "nextflow" + ], + "license": [ + "MIT" + ], + "name": [ + "nf-core/datasync" + ], + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" + }, + "sdPublisher": { + "@id": "https://nf-co.re/" + }, + "url": [ + "https://github.com/nf-core/datasync", + "https://nf-co.re/datasync/1.0.0/" + ], + "version": [ + "1.0.0" + ] + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", + "@type": "ComputerLanguage", + "identifier": { + "@id": "https://www.nextflow.io/" + }, + "name": "Nextflow", + "url": { + "@id": "https://www.nextflow.io/" + }, + "version": "!>=25.10.4" + }, + { + "@id": "#77ce8e20-3bfe-48e3-a2ef-1e81d74d71b6", + "@type": "TestSuite", + "instance": [ + { + "@id": "#c23bf1c1-9211-4368-a804-064620c06a63" + } + ], + "mainEntity": { + "@id": "main.nf" + }, + "name": "Test suite for nf-core/datasync" + }, + { + "@id": "#c23bf1c1-9211-4368-a804-064620c06a63", + "@type": "TestInstance", + "name": "GitHub Actions workflow for testing nf-core/datasync", + "resource": "repos/nf-core/datasync/actions/workflows/nf-test.yml", + "runsOn": { + "@id": "https://w3id.org/ro/terms/test#GithubService" + }, + "url": "https://api.github.com" + }, + { + "@id": "https://w3id.org/ro/terms/test#GithubService", + "@type": "TestService", + "name": "Github Actions", + "url": { + "@id": "https://github.com" + } + }, + { + "@id": "assets/", + "@type": "Dataset", + "description": "Additional files" + }, + { + "@id": "bin/", + "@type": "Dataset", + "description": "Scripts that must be callable from a pipeline process" + }, + { + "@id": "conf/", + "@type": "Dataset", + "description": "Configuration files" + }, + { + "@id": "docs/", + "@type": "Dataset", + "description": "Markdown files for documenting the pipeline" + }, + { + "@id": "docs/images/", + "@type": "Dataset", + "description": "Images for the documentation files" + }, + { + "@id": "modules/", + "@type": "Dataset", + "description": "Modules used by the pipeline" + }, + { + "@id": "modules/nf-core/", + "@type": "Dataset", + "description": "nf-core modules" + }, + { + "@id": "workflows/", + "@type": "Dataset", + "description": "Main pipeline workflows to be executed in main.nf" + }, + { + "@id": "subworkflows/", + "@type": "Dataset", + "description": "Smaller subworkflows" + }, + { + "@id": "nextflow.config", + "@type": "File", + "description": "Main Nextflow configuration file" + }, + { + "@id": "README.md", + "@type": "File", + "description": "Basic pipeline usage information" + }, + { + "@id": "nextflow_schema.json", + "@type": "File", + "description": "JSON schema for pipeline parameter specification" + }, + { + "@id": "CHANGELOG.md", + "@type": "File", + "description": "Information on changes made to the pipeline" + }, + { + "@id": "LICENSE", + "@type": "File", + "description": "The license - should be MIT" + }, + { + "@id": "CODE_OF_CONDUCT.md", + "@type": "File", + "description": "The nf-core code of conduct" + }, + { + "@id": "CITATIONS.md", + "@type": "File", + "description": "Citations needed when using the pipeline" + }, + { + "@id": "modules.json", + "@type": "File", + "description": "Version information for modules from nf-core/modules" + }, + { + "@id": "docs/usage.md", + "@type": "File", + "description": "Usage documentation" + }, + { + "@id": "docs/output.md", + "@type": "File", + "description": "Output documentation" + }, + { + "@id": ".nf-core.yml", + "@type": "File", + "description": "nf-core configuration file, configuring template features and linting rules" + }, + { + "@id": ".pre-commit-config.yaml", + "@type": "File", + "description": "Configuration file for pre-commit hooks" + }, + { + "@id": ".prettierignore", + "@type": "File", + "description": "Ignore file for prettier" + }, + { + "@id": "https://nf-co.re/", + "@type": "Organization", + "name": "nf-core", + "url": "https://nf-co.re/" + }, + { + "@id": "https://orcid.org/0000-0002-6503-2180", + "@type": "Person", + "email": "alexander.peltzer@boehringer-ingelheim.com", + "name": "Alexander Peltzer" + }, + { + "@id": "#be129ed0-c83e-444b-85dd-6db2c42dc277", + "@type": "Person", + "email": "antonia.saracco@zs.com", + "name": "Antonia Saracco" + }, + { + "@id": "#b293152b-1358-4678-a5a5-8603ccb89cd0", + "@type": "Person", + "email": "155591053+delfiterradas@users.noreply.github.com", + "name": "Delfina Terradas" + }, + { + "@id": "#6e1f504a-fae3-4fca-a7b7-8d84fff28bbd", + "@type": "Person", + "email": "18577080+atrigila@users.noreply.github.com", + "name": "Anabella Trigila" + }, + { + "@id": "#39fa8409-1f04-4472-9f46-7d3b03303768", + "@type": "Person", + "name": "Julian Schwab" + }, + { + "@id": "https://orcid.org/0000-0001-9584-7842", + "@type": "Person", + "email": "mail@gregor-sturm.de", + "name": "Gregor Sturm" + } + ] +} \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf b/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf index dc90ad9..965bc4c 100644 --- a/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// Subworkflow with functionality specific to the nf-core/datasync pipeline // /* @@ -8,38 +8,37 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' -include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet + help // boolean: Display help message and exit + help_full // boolean: Show the full help message + show_hidden // boolean: Show hidden parameters in the help message main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // Print version and exit if required and dump pipeline parameters to JSON file @@ -54,16 +53,43 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + + def before_text = "" + def after_text = "" + before_text = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m nf-core/datasync ${workflow.manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> " https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/datasync/blob/main/CITATIONS.md +""" + if (monochrome_logs) { + before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '') + } + + command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null, + help, + help_full, + show_hidden, + before_text, + after_text, + command, + null ) // @@ -72,6 +98,7 @@ workflow PIPELINE_INITIALISATION { UTILS_NFCORE_PIPELINE ( nextflow_cli_args ) + // // Custom validation for pipeline parameters // @@ -80,24 +107,9 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // - Channel - .fromSamplesheet("input") - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } - .groupTuple() - .map { - validateInputSamplesheet(it) - } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } + + channel + .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json")) .set { ch_samplesheet } emit: @@ -106,9 +118,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -119,88 +131,154 @@ workflow PIPELINE_COMPLETION { plaintext_email // boolean: Send plain-text email instead of HTML outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output - hook_url // string: hook URL for notifications multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + def multiqc_reports = multiqc_report.toList() // // Completion email and summary // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_reports.getVal(), + ) } completionSummary(monochrome_logs) - if (hook_url) { - imNotification(summary_params, hook_url) - } + } + + workflow.onError { + log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting" } } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +// +// Prepare samplesheet channels for rclone operations +// +def prepareSamplesheet(samplesheet) { + samplesheet.multiMap { meta, input_path, output_path, md5, sha -> + def normalized_input_path = input_path.toString().replaceFirst('^([a-zA-Z][a-zA-Z0-9+.-]*)://', '$1:') + def normalized_output_path = output_path.toString().replaceFirst('^([a-zA-Z][a-zA-Z0-9+.-]*)://', '$1:') + + def source = file(input_path) + + def rclone_destination = source.isFile() + ? normalized_output_path.replaceAll('/+$', '') + : "${normalized_output_path.replaceAll('/+$', '')}/${source.name}" + + def rclone_check = source.isFile() + ? normalized_input_path.replaceFirst('/[^/]+$', '') + : normalized_input_path.replaceAll('/+$', '') + + rclone: [ meta, normalized_input_path, rclone_destination ] + checksum: [ meta, md5, sha, rclone_check ] + } +} + // // Check and validate pipeline parameters // def validateInputParameters() { - genomeExistsError() -}// -// Validate channels from input samplesheet -// -def validateInputSamplesheet(input) { - def (metas, fastqs) = input[1..2] - // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 - if (!endedness_ok) { - error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + def samples = samplesheetToList(params.input, "${projectDir}/assets/schema_input.json") + + def requires_download = samples.any { meta, input_path, output_path, md5, sha -> + sha && (input_path ==~ /^[a-zA-Z][a-zA-Z0-9+.-]*:.*/) } - return [ metas[0], fastqs ] + if (requires_download && params.download) { + log.warn( + "The `--download` parameter is enabled. `RCLONE_CHECKSUM` will download remote files. " + + "Make sure this is what you want, as it may incur substantial cloud costs!" + ) + } + + if (requires_download && !params.download) { + log.error( + "A SHA checksum file was provided for one or more remote files, but `--download` " + + "is not enabled. `RCLONE_CHECKSUM` cannot verify SHA256 checksums for remote files " + + "without downloading them. Enable `--download` to proceed." + ) + exit 1 + } } + +// +// Create exit code summary // -// Get attribute from genome config file e.g. fasta +def createExitSummary(meta, exit_file, module) { + def code_map = [ + "0": "0 - Success", + "1": "1 - Error", + "2": "2 - Syntax or usage error", + "3": "3 - Directory not found", + "4": "4 - File not found", + "5": "5 - Temporary error", + "6": "6 - Less serious error", + "7": "7 - Fatal error", + "8": "8 - Transfer limit exceeded", + "9": "9 - No files transferred", + "10": "10 - Duration limit exceeded" + ] + def exit_code = exit_file.text.trim() + def code = code_map.get(exit_code, exit_code) + + [meta, "${meta.id}:${module}\t${meta.id}\t${module}\t${code}"] +} // -def getGenomeAttribute(attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] +// Parse Rclone check and checksum combined.txt file +// +def parseRcloneCheck(meta, check_file) { + def status_map = [ + '=': 'Match', + '-': 'Missing in source', + '+': 'Missing in destination', + '*': 'Mismatch', + '!': 'Error' + ] + def priority_map = [ + '!': 0, + '*': 1, + '-': 2, + '+': 3, + '=': 4 + ] + + return check_file.readLines() + .findAll { line -> line.trim() } + .collect { line -> + def fields = line.split(/ /, 2) + def status = status_map.get(fields[0], fields[0]) + def priority = priority_map.get(fields[0], 0) + + [ meta, "${meta.id}:${fields[1]}\t${status}\t${fields[1]}\t${meta.id}\t${priority}\n" ] } - } - return null } // -// Exit pipeline if incorrect --genome key provided -// -def genomeExistsError() { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - error(error_string) - } -}// // Generate methods description for MultiQC // def toolCitationText() { - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", + "Files were transferred to the specified destination using Rclone (Craig-Wood, 2023), which supports data movement across local and cloud storage backends.", + "File integrity was validated by computing cryptographic checksums with Rclone.", + "Pipeline results were summarised with MultiQC (Ewels et al. 2016)", "." ].join(' ').trim() @@ -208,34 +286,40 @@ def toolCitationText() { } def toolBibliographyText() { - // TODO nf-core: Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + "
  • Craig-Wood, N. (2023). Rclone: Rsync for cloud storage (Vers. 1.74.3). Computer software. https://rclone.org
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " ].join(' ').trim() return reference_text } def methodsDescriptionText(mqc_methods_yaml) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + // Convert to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = workflow.toMap() meta["manifest_map"] = workflow.manifest.toMap() // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + if (meta.manifest_map.doi) { + // Using a loop to handle multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + def temp_doi_ref = "" + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } + meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) + } else meta["doi_text"] = "" + meta["nodoi_text"] = meta.manifest_map.doi ?: "" // Tool references meta["tool_citations"] = "" meta["tool_bibliography"] = "" - // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - // meta["tool_bibliography"] = toolBibliographyText() + meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + meta["tool_bibliography"] = toolBibliographyText() def methods_text = mqc_methods_yaml.text diff --git a/subworkflows/local/utils_nfcore_datasync_pipeline/meta.yml b/subworkflows/local/utils_nfcore_datasync_pipeline/meta.yml new file mode 100644 index 0000000..ae7144f --- /dev/null +++ b/subworkflows/local/utils_nfcore_datasync_pipeline/meta.yml @@ -0,0 +1,69 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "PIPELINE_INITIALISATION" +description: Local utility subworkflow and functions for nf-core/datasync initialisation, completion, rclone report parsing, and MultiQC methods text. +keywords: + - utility + - datasync + - rclone + - multiqc +components: + - utils_nfschema_plugin + - completionemail + - completionsummary + - utils_nfcore_pipeline + - utils_nextflow_pipeline +input: + - version: + type: boolean + description: Display version and exit. + - validate_params: + type: boolean + description: Validate parameters against the schema at runtime. + - monochrome_logs: + type: boolean + description: Disable coloured log output. + - nextflow_cli_args: + type: list + description: Nextflow CLI positional arguments. + - outdir: + type: string + description: Output directory where results are saved. + - input: + type: string + description: Path to the input samplesheet. + - help: + type: boolean + description: Display help message and exit. + - help_full: + type: boolean + description: Display full help message. + - show_hidden: + type: boolean + description: Show hidden parameters in the help message. + - email: + type: string + description: Completion email address. + - email_on_fail: + type: string + description: Failure email address. + - plaintext_email: + type: boolean + description: Send plain-text email instead of HTML. + - multiqc_report: + type: file + description: MultiQC report emitted by the pipeline. +output: + - samplesheet: + type: file + description: Parsed samplesheet channel. + - versions: + type: file + description: Software versions channel. +authors: + - "@asaracco" + - "@delfiterradas" + - "@atrigila" +maintainers: + - "@asaracco" + - "@delfiterradas" + - "@atrigila" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28..37939ac 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,18 +2,13 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -26,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -49,16 +44,16 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -76,13 +71,25 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) - - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = workflow.launchDir.resolve(".${filename}") + def jsonGenerator = new groovy.json.JsonGenerator.Options() + .excludeNulls() + .addConverter(Path) { Path path -> path.toUriString() } + .addConverter(Duration) { Duration duration -> duration.toMillis() } + .addConverter(MemoryUnit) { MemoryUnit memory -> memory.toBytes() } + .addConverter(nextflow.script.types.VersionNumber) { nextflow.script.types.VersionNumber version -> version.toString() } + .build() + def jsonStr = jsonGenerator.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) + if (outdir instanceof Path) { + temp_pf.copyTo(outdir.resolve("pipeline_info/${filename}")) + } else if (outdir instanceof String) { + temp_pf.copyTo("${outdir}/pipeline_info/params_${timestamp}.json") + } else { + log.warn("Could not determine type of outdir, parameters JSON file will not be copied to output directory!") + } temp_pf.delete() } @@ -90,37 +97,42 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test index 8ed4310..68718e4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -51,4 +51,4 @@ nextflow_function { ) } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index db2030f..e3f0baf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -3,10 +3,18 @@ "content": [ "v9.9.9" ], - "timestamp": "2024-01-19T11:32:36.031083" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, - "timestamp": "2024-01-19T11:32:50.456" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index f7c54bc..02dbf09 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -11,9 +11,6 @@ nextflow_workflow { test("Should run no inputs") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = false @@ -39,9 +36,6 @@ nextflow_workflow { test("Should print version") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = true @@ -58,29 +52,28 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } test("Should dump params") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = 'results' check_conda_channels = false input[0] = false input[1] = true - input[2] = params.outdir + input[2] = outdir input[3] = false """ } @@ -96,19 +89,16 @@ nextflow_workflow { test("Should not create params JSON if no output directory") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = null check_conda_channels = false input[0] = false input[1] = true - input[2] = null + input[2] = outdir input[3] = false """ } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index 53574ff..a09572e 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml deleted file mode 100644 index f847611..0000000 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nextflow_pipeline: - - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a8b55d6..afca543 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,17 +2,13 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -21,27 +17,24 @@ workflow UTILS_NFCORE_PIPELINE { checkProfileProvided(nextflow_cli_args) emit: - valid_config + valid_config = valid_config } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -52,33 +45,22 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } -// -// Citation string for pipeline -// -def workflowCitation() { - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - " ${workflow.manifest.doi}\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -96,8 +78,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -107,8 +89,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -116,11 +98,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { processVersionsFromYAML(it) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML())) } // @@ -128,61 +106,40 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -194,79 +151,76 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } -// -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" +// Return a single report from an object that may be a Path or List +// +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() } + } else { + return null } - return mqc_report } // @@ -275,26 +229,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -311,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -331,40 +294,45 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -372,69 +340,16 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } -} - -// -// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack -// -def imNotification(summary_params, hook_url) { - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = getWorkflowVersion() - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("${workflow.projectDir}/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index 1dc317f..f117040 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -41,26 +41,14 @@ nextflow_function { } } - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { + test("Test Function without logColours") { - function "nfCoreLogo" + function "logColours" when { function { """ - input[0] = false + input[0] = true """ } } @@ -73,9 +61,8 @@ nextflow_function { } } - test("Test Function dashedLine") { - - function "dashedLine" + test("Test Function with logColours") { + function "logColours" when { function { @@ -93,14 +80,13 @@ nextflow_function { } } - test("Test Function without logColours") { - - function "logColours" + test("Test Function getSingleReport with a single file") { + function "getSingleReport" when { function { """ - input[0] = true + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) """ } } @@ -108,18 +94,22 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") } ) } } - test("Test Function with logColours") { - function "logColours" + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" when { function { """ - input[0] = false + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] """ } } @@ -127,7 +117,9 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 10f948e..02c6701 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -1,25 +1,21 @@ { "Test Function checkProfileProvided": { "content": null, - "timestamp": "2024-02-09T15:43:55.145717" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" }, "Test Function checkConfigProvided": { "content": [ true ], - "timestamp": "2024-01-19T11:34:13.548431224" - }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "timestamp": "2024-01-19T11:34:38.840454873" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "timestamp": "2024-01-19T11:34:22.24352016" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" }, "Test Function without logColours": { "content": [ @@ -73,13 +69,11 @@ "biwhite": "" } ], - "timestamp": "2024-01-19T11:35:04.418416984" - }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "timestamp": "2024-01-19T11:34:55.420000755" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" }, "Test Function with logColours": { "content": [ @@ -133,6 +127,10 @@ "biwhite": "\u001b[1;97m" } ], - "timestamp": "2024-01-19T11:35:13.436366565" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test new file mode 100644 index 0000000..8940d32 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap new file mode 100644 index 0000000..859d103 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap @@ -0,0 +1,19 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap index d07ce54..859d103 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -10,6 +10,10 @@ ] } ], - "timestamp": "2024-01-19T11:35:22.538940073" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml deleted file mode 100644 index ac8523c..0000000 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfcore_pipeline: - - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 0000000..9ff0681 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,77 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + help // boolean: show help message + help_full // boolean: show full help message + show_hidden // boolean: show hidden parameters in help message + before_text // string: text to show before the help message and parameters summary + after_text // string: text to show after the help message and parameters summary + command // string: an example command of the pipeline + cli_typecast // boolean: whether to perform typecasting of CLI parameters. Set this to `null` to use the default behaviour + + main: + + if(help || help_full) { + help_options = [ + beforeText: before_text, + afterText: after_text, + command: command, + showHidden: show_hidden, + fullHelp: help_full, + ] + if(parameters_schema) { + help_options << [parameters_schema: parameters_schema] + } + log.info paramsHelp( + help_options, + (help instanceof String && help != "true") ? help : "", + ) + exit 0 + } + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + + summary_options = [:] + if(parameters_schema) { + summary_options << [parameters_schema: parameters_schema] + } + log.info before_text + log.info paramsSummaryLog(summary_options, input_workflow) + log.info after_text + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + validateOptions = [:] + if(parameters_schema) { + validateOptions << [parameters_schema: parameters_schema] + } + if(cli_typecast != null) { + validateOptions << [cast_cli_params: cli_typecast] + } + validateParameters(validateOptions) + } + + emit: + dummy_emit = true +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 0000000..1d8c75a --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,59 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. + - help: + type: boolean, string + description: | + Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message. + - help_full: + type: boolean + description: Show the full help message and exit. + - show_hidden: + type: boolean + description: Show hidden parameters in the help message. + - before_text: + type: string + description: Text to show before the parameters summary and help message. + - after_text: + type: string + description: Text to show after the parameters summary and help message. + - command: + type: string + description: An example command to run the pipeline, to show in the help message and the summary. + - cli_typecast: + type: boolean + description: | + Whether to apply typecasting to the parameters given via the CLI before validation. + Set this to `null` to use the default behavior. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 0000000..1fd1eac --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,178 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should create a help message") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = true + input[4] = false + input[5] = false + input[6] = "Before" + input[7] = "After" + input[8] = "nextflow run test/test" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 0000000..fd71cb8 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.7.2" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 93% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c..e1fa4e2 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/./main/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b0..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 517ee54..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cff..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/tests/.nftignore b/tests/.nftignore new file mode 100644 index 0000000..b1e73cd --- /dev/null +++ b/tests/.nftignore @@ -0,0 +1,13 @@ +.DS_Store +multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt +multiqc/multiqc_data/multiqc.parquet +multiqc/multiqc_data/multiqc.log +multiqc/multiqc_data/multiqc_data.json +multiqc/multiqc_data/multiqc_sources.txt +multiqc/multiqc_data/multiqc_software_versions.txt +multiqc/multiqc_data/llms-full.txt +multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} +multiqc/multiqc_report.html +fastqc/*_fastqc.{html,zip} +pipeline_info/*.{html,json,txt,yml} +rclone/**/*.log diff --git a/tests/assets/real_copy_samplesheet.csv b/tests/assets/real_copy_samplesheet.csv new file mode 100644 index 0000000..0704889 --- /dev/null +++ b/tests/assets/real_copy_samplesheet.csv @@ -0,0 +1,5 @@ +sample,input,output_path,checksum_md5,checksum_sha +Illumina_annotation_missing,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Annotation/Archives/,./results/destination/,https://raw.githubusercontent.com/nf-core/test-datasets/datasync/test-data/Illumina_annotation_missing_md5.tsv, +Illumina_annotation_incorrect,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Annotation/Archives/,./results/destination/,https://raw.githubusercontent.com/nf-core/test-datasets/datasync/test-data/Illumina_annotation_incorrect_md5.tsv, +Illumina_annotation_sha_only,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Annotation/Archives/,./results/destination/,,https://raw.githubusercontent.com/nf-core/test-datasets/datasync/test-data/Illumina_annotation_incorrect_sha.tsv +benchmark_bed,gs://deepvariant/GIAB_v5q0/HG002_GRCh38_v5.0q_smvar.benchmark.bed,./results/destination/,https://raw.githubusercontent.com/nf-core/test-datasets/datasync/test-data/bed_md5.tsv diff --git a/tests/default.nf.test b/tests/default.nf.test new file mode 100644 index 0000000..0178b64 --- /dev/null +++ b/tests/default.nf.test @@ -0,0 +1,39 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + profile "test" + + test("-profile test") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // Summarise rclone outputs by line count + def rclone_reports = getAllFilesFromDir(params.outdir, relative: true, include: ['rclone/**/*.txt']) + def rclone_line_counts = rclone_reports.findAll { !it.endsWith('.exit_code.txt') }.collect { file -> "${file.tokenize('/').last()}:lines,${path("${params.outdir}/${file}").csv(header: false).rowCount}" } + assertAll( + { assert workflow.success }, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_datasync_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_path, + // All files with stable contents + stable_content, + // Number of lines in each rclone check and checksum output + rclone_line_counts + ).match() } + ) + } + } +} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 0000000..1b63cec --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,97 @@ +{ + "-profile test": { + "content": [ + { + "RCLONE_CHECK": { + "rclone": "1.74.3-DEV" + }, + "RCLONE_CHECKSUM": { + "rclone": "1.74.3-DEV" + }, + "RCLONE_COPY": { + "rclone": "1.74.3-DEV" + }, + "Workflow": { + "nf-core/datasync": "v1.0.0" + } + }, + [ + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_rclone_check.txt", + "multiqc/multiqc_data/multiqc_rclone_checksum_md5.txt", + "multiqc/multiqc_data/multiqc_rclone_exit_codes.txt", + "multiqc/multiqc_data/multiqc_samplesheet.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_datasync_software_mqc_versions.yml", + "rclone", + "rclone/check_after", + "rclone/check_after/Illumina_annotation", + "rclone/check_after/Illumina_annotation/Illumina_annotation_check.combined.txt", + "rclone/check_after/Illumina_annotation/Illumina_annotation_check.exit_code.txt", + "rclone/check_after/Illumina_annotation/Illumina_annotation_check.match.txt", + "rclone/check_after/benchmark_bed", + "rclone/check_after/benchmark_bed/benchmark_bed_check.combined.txt", + "rclone/check_after/benchmark_bed/benchmark_bed_check.exit_code.txt", + "rclone/check_after/benchmark_bed/benchmark_bed_check.match.txt", + "rclone/checksum_before", + "rclone/checksum_before/Illumina_annotation", + "rclone/checksum_before/Illumina_annotation/Illumina_annotation_checksum_MD5.combined.txt", + "rclone/checksum_before/Illumina_annotation/Illumina_annotation_checksum_MD5.exit_code.txt", + "rclone/checksum_before/Illumina_annotation/Illumina_annotation_checksum_MD5.match.txt", + "rclone/checksum_before/benchmark_bed", + "rclone/checksum_before/benchmark_bed/benchmark_bed_checksum_MD5.combined.txt", + "rclone/checksum_before/benchmark_bed/benchmark_bed_checksum_MD5.exit_code.txt", + "rclone/checksum_before/benchmark_bed/benchmark_bed_checksum_MD5.match.txt", + "rclone/checksum_before/benchmark_bed/benchmark_bed_checksum_MD5.missing_on_src.txt", + "rclone/copy", + "rclone/copy/Illumina_annotation-rclone-copy.log", + "rclone/copy/benchmark_bed-rclone-copy.log" + ], + [ + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_rclone_check.txt:md5,f9dc48d3c4d35cd7297b0a16227c3bcd", + "multiqc_rclone_checksum_md5.txt:md5,c7127de966d1be295ef6697dba648c79", + "multiqc_rclone_exit_codes.txt:md5,d970d9335584ff1e7349036e62f5e8d4", + "multiqc_samplesheet.txt:md5,373d903a41ab29bd26db35a3041626e4", + "Illumina_annotation_check.combined.txt:md5,bbb93addf748c7c6cbe5ad1e25bf54bb", + "Illumina_annotation_check.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "Illumina_annotation_check.match.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "benchmark_bed_check.combined.txt:md5,dcd2c539696adba720986251dcd1aaef", + "benchmark_bed_check.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "benchmark_bed_check.match.txt:md5,12608858576bec12c65ff338a99803c3", + "Illumina_annotation_checksum_MD5.combined.txt:md5,bbb93addf748c7c6cbe5ad1e25bf54bb", + "Illumina_annotation_checksum_MD5.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "Illumina_annotation_checksum_MD5.match.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "benchmark_bed_checksum_MD5.combined.txt:md5,592b2b2af44551686a8057f585309413", + "benchmark_bed_checksum_MD5.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1", + "benchmark_bed_checksum_MD5.match.txt:md5,12608858576bec12c65ff338a99803c3", + "benchmark_bed_checksum_MD5.missing_on_src.txt:md5,7bf2def3eed9eff615a0f29ae1652254" + ], + [ + "Illumina_annotation_check.combined.txt:lines,15", + "Illumina_annotation_check.match.txt:lines,15", + "benchmark_bed_check.combined.txt:lines,1", + "benchmark_bed_check.match.txt:lines,1", + "Illumina_annotation_checksum_MD5.combined.txt:lines,15", + "Illumina_annotation_checksum_MD5.match.txt:lines,15", + "benchmark_bed_checksum_MD5.combined.txt:lines,10", + "benchmark_bed_checksum_MD5.match.txt:lines,1", + "benchmark_bed_checksum_MD5.missing_on_src.txt:lines,9" + ] + ], + "timestamp": "2026-09-25T22:09:52.86634064", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/tests/edge.nf.test b/tests/edge.nf.test new file mode 100644 index 0000000..b6e3fef --- /dev/null +++ b/tests/edge.nf.test @@ -0,0 +1,99 @@ +nextflow_pipeline { + + name "Test pipeline edge cases" + script "../main.nf" + tag "pipeline" + tag "edge" + profile "test" + + test("-profile test edge cases") { + + when { + params { + input = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/datasync/test-data/samplesheet_edge.csv" + outdir = "$outputDir" + download = true + } + } + + then { + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def nextflow_log = path("${launchDir}/meta/nextflow.log").text + // Summarise rclone outputs by line count + def rclone_reports = getAllFilesFromDir(params.outdir, relative: true, include: ['rclone/**/*.txt']) + def rclone_line_counts = rclone_reports.findAll { !it.endsWith('.exit_code.txt') }.collect { file -> "${file.tokenize('/').last()}:lines,${path("${params.outdir}/${file}").csv(header: false).rowCount}" } + assertAll( + { assert workflow.success }, + { assert nextflow_log.contains("The `--download` parameter is enabled") }, + { assert nextflow_log.contains("it may incur substantial cloud costs") }, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_datasync_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_path, + // All files with stable contents + stable_content, + // Number of lines in each rclone check and checksum output + rclone_line_counts + ).match() } + ) + } + } + + test("-profile test copy matching files only") { + + when { + params { + input = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/datasync/test-data/samplesheet_edge.csv" + outdir = "$outputDir" + copy_matching_only = true + download = true + } + } + + then { + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // Summarise rclone outputs by line count + def rclone_line_counts = getAllFilesFromDir(params.outdir, relative: true, include: ['rclone/**/*.txt']) + rclone_line_counts = rclone_line_counts.collect { file -> "${file.tokenize('/').last()}:lines,${path("${params.outdir}/${file}").csv(header: false).rowCount}" } + assertAll( + { assert workflow.success }, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_datasync_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_path, + // All files with stable contents + stable_content, + // Number of lines in each rclone check and checksum output + rclone_line_counts + ).match() } + ) + } + } + + test("-profile test remote source with SHA256 checksums - fail") { + + when { + params { + input = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/datasync/test-data/samplesheet_edge.csv" + outdir = "$outputDir" + } + } + + then { + def nextflow_log = path("${launchDir}/meta/nextflow.log").text + assertAll( + { assert workflow.failed }, + { assert nextflow_log.contains("A SHA checksum file was provided for one or more remote files") }, + { assert nextflow_log.contains("Enable `--download` to proceed") } + ) + } + } +} diff --git a/tests/edge.nf.test.snap b/tests/edge.nf.test.snap new file mode 100644 index 0000000..fe36703 --- /dev/null +++ b/tests/edge.nf.test.snap @@ -0,0 +1,254 @@ +{ + "-profile test copy matching files only": { + "content": [ + { + "RCLONE_CHECK": { + "rclone": "1.74.3-DEV" + }, + "RCLONE_CHECKSUM": { + "rclone": "1.74.3-DEV" + }, + "RCLONE_COPY": { + "rclone": "1.74.3-DEV" + }, + "Workflow": { + "nf-core/datasync": "v1.0.0" + } + }, + [ + "create", + "create/files_to_copy.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_rclone_check.txt", + "multiqc/multiqc_data/multiqc_rclone_checksum_md5.txt", + "multiqc/multiqc_data/multiqc_rclone_checksum_sha.txt", + "multiqc/multiqc_data/multiqc_rclone_exit_codes.txt", + "multiqc/multiqc_data/multiqc_samplesheet.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_datasync_software_mqc_versions.yml", + "rclone", + "rclone/check_after", + "rclone/check_after/Illumina_annotation_incorrect", + "rclone/check_after/Illumina_annotation_incorrect/Illumina_annotation_incorrect_check.combined.txt", + "rclone/check_after/Illumina_annotation_incorrect/Illumina_annotation_incorrect_check.exit_code.txt", + "rclone/check_after/Illumina_annotation_incorrect/Illumina_annotation_incorrect_check.match.txt", + "rclone/check_after/Illumina_annotation_missing", + "rclone/check_after/Illumina_annotation_missing/Illumina_annotation_missing_check.combined.txt", + "rclone/check_after/Illumina_annotation_missing/Illumina_annotation_missing_check.exit_code.txt", + "rclone/check_after/Illumina_annotation_missing/Illumina_annotation_missing_check.match.txt", + "rclone/check_after/Illumina_annotation_sha_only", + "rclone/check_after/Illumina_annotation_sha_only/Illumina_annotation_sha_only_check.combined.txt", + "rclone/check_after/Illumina_annotation_sha_only/Illumina_annotation_sha_only_check.exit_code.txt", + "rclone/check_after/Illumina_annotation_sha_only/Illumina_annotation_sha_only_check.match.txt", + "rclone/checksum_before", + "rclone/checksum_before/Illumina_annotation_incorrect", + "rclone/checksum_before/Illumina_annotation_incorrect/Illumina_annotation_incorrect_checksum_MD5.combined.txt", + "rclone/checksum_before/Illumina_annotation_incorrect/Illumina_annotation_incorrect_checksum_MD5.differ.txt", + "rclone/checksum_before/Illumina_annotation_incorrect/Illumina_annotation_incorrect_checksum_MD5.exit_code.txt", + "rclone/checksum_before/Illumina_annotation_incorrect/Illumina_annotation_incorrect_checksum_MD5.match.txt", + "rclone/checksum_before/Illumina_annotation_missing", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.combined.txt", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.exit_code.txt", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.match.txt", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.missing_on_dst.txt", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.missing_on_src.txt", + "rclone/checksum_before/Illumina_annotation_sha_only", + "rclone/checksum_before/Illumina_annotation_sha_only/Illumina_annotation_sha_only_checksum_SHA256.combined.txt", + "rclone/checksum_before/Illumina_annotation_sha_only/Illumina_annotation_sha_only_checksum_SHA256.differ.txt", + "rclone/checksum_before/Illumina_annotation_sha_only/Illumina_annotation_sha_only_checksum_SHA256.exit_code.txt", + "rclone/copy", + "rclone/copy/Illumina_annotation_incorrect-rclone-copy.log", + "rclone/copy/Illumina_annotation_missing-rclone-copy.log" + ], + [ + "files_to_copy.txt:md5,df576e44dfe5a24521997ef162cba157", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_rclone_check.txt:md5,c8f13c10aa4f0e4b356c5c08a9ae7ee9", + "multiqc_rclone_checksum_md5.txt:md5,40ef26b67a9f5c4943a12d412f4e632f", + "multiqc_rclone_checksum_sha.txt:md5,8d38305a4ad03c7ea18aa9827d34a396", + "multiqc_rclone_exit_codes.txt:md5,3dd8d4741882ff589545c2f2fcc99520", + "multiqc_samplesheet.txt:md5,bbfc817ff43c49cde14a2b33f46b5ae5", + "Illumina_annotation_incorrect_check.combined.txt:md5,bbb93addf748c7c6cbe5ad1e25bf54bb", + "Illumina_annotation_incorrect_check.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "Illumina_annotation_incorrect_check.match.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "Illumina_annotation_missing_check.combined.txt:md5,bbb93addf748c7c6cbe5ad1e25bf54bb", + "Illumina_annotation_missing_check.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "Illumina_annotation_missing_check.match.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "Illumina_annotation_sha_only_check.combined.txt:md5,bbb93addf748c7c6cbe5ad1e25bf54bb", + "Illumina_annotation_sha_only_check.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "Illumina_annotation_sha_only_check.match.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "Illumina_annotation_incorrect_checksum_MD5.combined.txt:md5,34ecbd1fa8f707c75898ee45cadf45d6", + "Illumina_annotation_incorrect_checksum_MD5.differ.txt:md5,e5fdf362a1dc4ac877f92ee769e47fd8", + "Illumina_annotation_incorrect_checksum_MD5.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1", + "Illumina_annotation_incorrect_checksum_MD5.match.txt:md5,df576e44dfe5a24521997ef162cba157", + "Illumina_annotation_missing_checksum_MD5.combined.txt:md5,4030b978509bbd39819efab4d91d7f32", + "Illumina_annotation_missing_checksum_MD5.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1", + "Illumina_annotation_missing_checksum_MD5.match.txt:md5,df576e44dfe5a24521997ef162cba157", + "Illumina_annotation_missing_checksum_MD5.missing_on_dst.txt:md5,793e4b78c8b125e4421cb20ed0c232d5", + "Illumina_annotation_missing_checksum_MD5.missing_on_src.txt:md5,e5fdf362a1dc4ac877f92ee769e47fd8", + "Illumina_annotation_sha_only_checksum_SHA256.combined.txt:md5,0d2bc4aeee4fded37d5cfebfadfb2fd2", + "Illumina_annotation_sha_only_checksum_SHA256.differ.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "Illumina_annotation_sha_only_checksum_SHA256.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1" + ], + [ + "Illumina_annotation_incorrect_check.combined.txt:lines,15", + "Illumina_annotation_incorrect_check.exit_code.txt:lines,1", + "Illumina_annotation_incorrect_check.match.txt:lines,15", + "Illumina_annotation_missing_check.combined.txt:lines,15", + "Illumina_annotation_missing_check.exit_code.txt:lines,1", + "Illumina_annotation_missing_check.match.txt:lines,15", + "Illumina_annotation_sha_only_check.combined.txt:lines,15", + "Illumina_annotation_sha_only_check.exit_code.txt:lines,1", + "Illumina_annotation_sha_only_check.match.txt:lines,15", + "Illumina_annotation_incorrect_checksum_MD5.combined.txt:lines,15", + "Illumina_annotation_incorrect_checksum_MD5.differ.txt:lines,5", + "Illumina_annotation_incorrect_checksum_MD5.exit_code.txt:lines,1", + "Illumina_annotation_incorrect_checksum_MD5.match.txt:lines,10", + "Illumina_annotation_missing_checksum_MD5.combined.txt:lines,16", + "Illumina_annotation_missing_checksum_MD5.exit_code.txt:lines,1", + "Illumina_annotation_missing_checksum_MD5.match.txt:lines,10", + "Illumina_annotation_missing_checksum_MD5.missing_on_dst.txt:lines,1", + "Illumina_annotation_missing_checksum_MD5.missing_on_src.txt:lines,5", + "Illumina_annotation_sha_only_checksum_SHA256.combined.txt:lines,15", + "Illumina_annotation_sha_only_checksum_SHA256.differ.txt:lines,15", + "Illumina_annotation_sha_only_checksum_SHA256.exit_code.txt:lines,1" + ] + ], + "timestamp": "2026-09-25T22:10:33.913797083", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "-profile test edge cases": { + "content": [ + { + "RCLONE_CHECK": { + "rclone": "1.74.3-DEV" + }, + "RCLONE_CHECKSUM": { + "rclone": "1.74.3-DEV" + }, + "RCLONE_COPY": { + "rclone": "1.74.3-DEV" + }, + "Workflow": { + "nf-core/datasync": "v1.0.0" + } + }, + [ + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_rclone_check.txt", + "multiqc/multiqc_data/multiqc_rclone_checksum_md5.txt", + "multiqc/multiqc_data/multiqc_rclone_checksum_sha.txt", + "multiqc/multiqc_data/multiqc_rclone_exit_codes.txt", + "multiqc/multiqc_data/multiqc_samplesheet.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_datasync_software_mqc_versions.yml", + "rclone", + "rclone/check_after", + "rclone/check_after/Illumina_annotation_incorrect", + "rclone/check_after/Illumina_annotation_incorrect/Illumina_annotation_incorrect_check.combined.txt", + "rclone/check_after/Illumina_annotation_incorrect/Illumina_annotation_incorrect_check.exit_code.txt", + "rclone/check_after/Illumina_annotation_incorrect/Illumina_annotation_incorrect_check.match.txt", + "rclone/check_after/Illumina_annotation_missing", + "rclone/check_after/Illumina_annotation_missing/Illumina_annotation_missing_check.combined.txt", + "rclone/check_after/Illumina_annotation_missing/Illumina_annotation_missing_check.exit_code.txt", + "rclone/check_after/Illumina_annotation_missing/Illumina_annotation_missing_check.match.txt", + "rclone/check_after/Illumina_annotation_sha_only", + "rclone/check_after/Illumina_annotation_sha_only/Illumina_annotation_sha_only_check.combined.txt", + "rclone/check_after/Illumina_annotation_sha_only/Illumina_annotation_sha_only_check.exit_code.txt", + "rclone/check_after/Illumina_annotation_sha_only/Illumina_annotation_sha_only_check.match.txt", + "rclone/checksum_before", + "rclone/checksum_before/Illumina_annotation_incorrect", + "rclone/checksum_before/Illumina_annotation_incorrect/Illumina_annotation_incorrect_checksum_MD5.combined.txt", + "rclone/checksum_before/Illumina_annotation_incorrect/Illumina_annotation_incorrect_checksum_MD5.differ.txt", + "rclone/checksum_before/Illumina_annotation_incorrect/Illumina_annotation_incorrect_checksum_MD5.exit_code.txt", + "rclone/checksum_before/Illumina_annotation_incorrect/Illumina_annotation_incorrect_checksum_MD5.match.txt", + "rclone/checksum_before/Illumina_annotation_missing", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.combined.txt", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.exit_code.txt", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.match.txt", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.missing_on_dst.txt", + "rclone/checksum_before/Illumina_annotation_missing/Illumina_annotation_missing_checksum_MD5.missing_on_src.txt", + "rclone/checksum_before/Illumina_annotation_sha_only", + "rclone/checksum_before/Illumina_annotation_sha_only/Illumina_annotation_sha_only_checksum_SHA256.combined.txt", + "rclone/checksum_before/Illumina_annotation_sha_only/Illumina_annotation_sha_only_checksum_SHA256.differ.txt", + "rclone/checksum_before/Illumina_annotation_sha_only/Illumina_annotation_sha_only_checksum_SHA256.exit_code.txt", + "rclone/copy", + "rclone/copy/Illumina_annotation_incorrect-rclone-copy.log", + "rclone/copy/Illumina_annotation_missing-rclone-copy.log", + "rclone/copy/Illumina_annotation_sha_only-rclone-copy.log" + ], + [ + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_rclone_check.txt:md5,c8f13c10aa4f0e4b356c5c08a9ae7ee9", + "multiqc_rclone_checksum_md5.txt:md5,40ef26b67a9f5c4943a12d412f4e632f", + "multiqc_rclone_checksum_sha.txt:md5,8d38305a4ad03c7ea18aa9827d34a396", + "multiqc_rclone_exit_codes.txt:md5,3dd8d4741882ff589545c2f2fcc99520", + "multiqc_samplesheet.txt:md5,bbfc817ff43c49cde14a2b33f46b5ae5", + "Illumina_annotation_incorrect_check.combined.txt:md5,bbb93addf748c7c6cbe5ad1e25bf54bb", + "Illumina_annotation_incorrect_check.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "Illumina_annotation_incorrect_check.match.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "Illumina_annotation_missing_check.combined.txt:md5,bbb93addf748c7c6cbe5ad1e25bf54bb", + "Illumina_annotation_missing_check.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "Illumina_annotation_missing_check.match.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "Illumina_annotation_sha_only_check.combined.txt:md5,bbb93addf748c7c6cbe5ad1e25bf54bb", + "Illumina_annotation_sha_only_check.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "Illumina_annotation_sha_only_check.match.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "Illumina_annotation_incorrect_checksum_MD5.combined.txt:md5,34ecbd1fa8f707c75898ee45cadf45d6", + "Illumina_annotation_incorrect_checksum_MD5.differ.txt:md5,e5fdf362a1dc4ac877f92ee769e47fd8", + "Illumina_annotation_incorrect_checksum_MD5.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1", + "Illumina_annotation_incorrect_checksum_MD5.match.txt:md5,df576e44dfe5a24521997ef162cba157", + "Illumina_annotation_missing_checksum_MD5.combined.txt:md5,4030b978509bbd39819efab4d91d7f32", + "Illumina_annotation_missing_checksum_MD5.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1", + "Illumina_annotation_missing_checksum_MD5.match.txt:md5,df576e44dfe5a24521997ef162cba157", + "Illumina_annotation_missing_checksum_MD5.missing_on_dst.txt:md5,793e4b78c8b125e4421cb20ed0c232d5", + "Illumina_annotation_missing_checksum_MD5.missing_on_src.txt:md5,e5fdf362a1dc4ac877f92ee769e47fd8", + "Illumina_annotation_sha_only_checksum_SHA256.combined.txt:md5,0d2bc4aeee4fded37d5cfebfadfb2fd2", + "Illumina_annotation_sha_only_checksum_SHA256.differ.txt:md5,eb40be996bfbcf8070103efaa6bfa4c5", + "Illumina_annotation_sha_only_checksum_SHA256.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1" + ], + [ + "Illumina_annotation_incorrect_check.combined.txt:lines,15", + "Illumina_annotation_incorrect_check.match.txt:lines,15", + "Illumina_annotation_missing_check.combined.txt:lines,15", + "Illumina_annotation_missing_check.match.txt:lines,15", + "Illumina_annotation_sha_only_check.combined.txt:lines,15", + "Illumina_annotation_sha_only_check.match.txt:lines,15", + "Illumina_annotation_incorrect_checksum_MD5.combined.txt:lines,15", + "Illumina_annotation_incorrect_checksum_MD5.differ.txt:lines,5", + "Illumina_annotation_incorrect_checksum_MD5.match.txt:lines,10", + "Illumina_annotation_missing_checksum_MD5.combined.txt:lines,16", + "Illumina_annotation_missing_checksum_MD5.match.txt:lines,10", + "Illumina_annotation_missing_checksum_MD5.missing_on_dst.txt:lines,1", + "Illumina_annotation_missing_checksum_MD5.missing_on_src.txt:lines,5", + "Illumina_annotation_sha_only_checksum_SHA256.combined.txt:lines,15", + "Illumina_annotation_sha_only_checksum_SHA256.differ.txt:lines,15" + ] + ], + "timestamp": "2026-09-25T22:10:13.501072101", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/tests/main_full.nf.test b/tests/main_full.nf.test new file mode 100644 index 0000000..42b21df --- /dev/null +++ b/tests/main_full.nf.test @@ -0,0 +1,39 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + profile "test_full" + + test("-profile test_full") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // Summarise rclone outputs by line count + def rclone_reports = getAllFilesFromDir(params.outdir, relative: true, include: ['rclone/**/*.txt']) + def rclone_line_counts = rclone_reports.findAll { !it.endsWith('.exit_code.txt') }.collect { file -> "${file.tokenize('/').last()}:lines,${path("${params.outdir}/${file}").csv(header: false).rowCount}" } + assertAll( + { assert workflow.success }, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_datasync_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_path, + // All files with stable contents + stable_content, + // Number of lines in each rclone check and checksum output + rclone_line_counts + ).match() } + ) + } + } +} diff --git a/tests/main_full.nf.test.snap b/tests/main_full.nf.test.snap new file mode 100644 index 0000000..fc2adf1 --- /dev/null +++ b/tests/main_full.nf.test.snap @@ -0,0 +1,88 @@ +{ + "-profile test_full": { + "content": [ + { + "RCLONE_CHECK": { + "rclone": "1.74.3-DEV" + }, + "RCLONE_CHECKSUM": { + "rclone": "1.74.3-DEV" + }, + "RCLONE_COPY": { + "rclone": "1.74.3-DEV" + }, + "Workflow": { + "nf-core/datasync": "v1.0.0" + } + }, + [ + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_rclone_check.txt", + "multiqc/multiqc_data/multiqc_rclone_checksum_md5.txt", + "multiqc/multiqc_data/multiqc_rclone_checksum_sha.txt", + "multiqc/multiqc_data/multiqc_rclone_exit_codes.txt", + "multiqc/multiqc_data/multiqc_samplesheet.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_datasync_software_mqc_versions.yml", + "rclone", + "rclone/check_after", + "rclone/check_after/demultiplex", + "rclone/check_after/demultiplex/demultiplex_check.combined.txt", + "rclone/check_after/demultiplex/demultiplex_check.exit_code.txt", + "rclone/check_after/demultiplex/demultiplex_check.match.txt", + "rclone/checksum_before", + "rclone/checksum_before/demultiplex", + "rclone/checksum_before/demultiplex/demultiplex_checksum_MD5.combined.txt", + "rclone/checksum_before/demultiplex/demultiplex_checksum_MD5.exit_code.txt", + "rclone/checksum_before/demultiplex/demultiplex_checksum_MD5.match.txt", + "rclone/checksum_before/demultiplex/demultiplex_checksum_MD5.missing_on_src.txt", + "rclone/checksum_before/demultiplex/demultiplex_checksum_SHA256.combined.txt", + "rclone/checksum_before/demultiplex/demultiplex_checksum_SHA256.exit_code.txt", + "rclone/checksum_before/demultiplex/demultiplex_checksum_SHA256.match.txt", + "rclone/copy", + "rclone/copy/demultiplex-rclone-copy.log" + ], + [ + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_rclone_check.txt:md5,03a73f087a286ec6580aada2a5db2e7c", + "multiqc_rclone_checksum_md5.txt:md5,a68bd0275b5b6cb62ec966b68121b0e1", + "multiqc_rclone_checksum_sha.txt:md5,03a73f087a286ec6580aada2a5db2e7c", + "multiqc_rclone_exit_codes.txt:md5,2bc7209227358c54fa71dc3adb38d159", + "multiqc_samplesheet.txt:md5,00788a52d1a014c12ac4ed554b0b44ca", + "demultiplex_check.combined.txt:md5,3ae32d27ed8a8e14c3b9b954e23c3839", + "demultiplex_check.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "demultiplex_check.match.txt:md5,902e4715d579b7f43a5463a220df8db0", + "demultiplex_checksum_MD5.combined.txt:md5,9250a5e20244b4beb397eab1a2003c3a", + "demultiplex_checksum_MD5.exit_code.txt:md5,b026324c6904b2a9cb4b88d6d61c81d1", + "demultiplex_checksum_MD5.match.txt:md5,644b95db936b45b931143faefb15be7f", + "demultiplex_checksum_MD5.missing_on_src.txt:md5,b9f072c9e776951c6759590a8259f765", + "demultiplex_checksum_SHA256.combined.txt:md5,3ae32d27ed8a8e14c3b9b954e23c3839", + "demultiplex_checksum_SHA256.exit_code.txt:md5,897316929176464ebc9ad085f31e7284", + "demultiplex_checksum_SHA256.match.txt:md5,902e4715d579b7f43a5463a220df8db0" + ], + [ + "demultiplex_check.combined.txt:lines,538", + "demultiplex_check.match.txt:lines,538", + "demultiplex_checksum_MD5.combined.txt:lines,538", + "demultiplex_checksum_MD5.match.txt:lines,502", + "demultiplex_checksum_MD5.missing_on_src.txt:lines,36", + "demultiplex_checksum_SHA256.combined.txt:lines,538", + "demultiplex_checksum_SHA256.match.txt:lines,538" + ] + ], + "timestamp": "2026-09-25T22:12:32.711478602", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 0000000..b912e04 --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,14 @@ +/* +======================================================================================== + Nextflow config file for running nf-test tests +======================================================================================== +*/ + +// Or any resources requirements +params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/datasync/' +} + +// Fixes S3 access issues on self-hosted runners +aws.client.anonymous = true diff --git a/workflows/datasync.nf b/workflows/datasync.nf index 49f36c1..cb7a6d9 100644 --- a/workflows/datasync.nf +++ b/workflows/datasync.nf @@ -3,13 +3,18 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_datasync_pipeline' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { RCLONE_COPY } from '../modules/nf-core/rclone/copy/main' +include { RCLONE_CHECK } from '../modules/nf-core/rclone/check/main' +include { RCLONE_CHECKSUM } from '../modules/nf-core/rclone/checksum/main' +include { CREATE_FILTER_LIST } from '../modules/local/create_filter_list/main' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_datasync_pipeline' +include { parseRcloneCheck } from '../subworkflows/local/utils_nfcore_datasync_pipeline' +include { createExitSummary } from '../subworkflows/local/utils_nfcore_datasync_pipeline' +include { prepareSamplesheet } from '../subworkflows/local/utils_nfcore_datasync_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -21,51 +26,196 @@ workflow DATASYNC { take: ch_samplesheet // channel: samplesheet read in from --input + multiqc_config + multiqc_logo + multiqc_methods_description + outdir + rclone_config main: - ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() + ch_versions = channel.empty() + ch_multiqc_files = channel.empty() + ch_rclone_config = rclone_config ? file(rclone_config, checkIfExists: true) : [] + + ch_samplesheet = prepareSamplesheet(ch_samplesheet) + ch_rclone = ch_samplesheet.rclone + + // Group input md5sum/shasum with their respective generated checksum + ch_checksum = ch_samplesheet.checksum + .flatMap { meta, md5, sha, input -> + def checksum_tuple = [] + if (md5) { + checksum_tuple << tuple(meta + [check_format: "md5"], md5, 'MD5', input) + } + if (sha) { + checksum_tuple << tuple(meta + [check_format: "sha"], sha, "SHA256", input) + } + + return checksum_tuple + } + + RCLONE_CHECKSUM( + ch_checksum, + ch_rclone_config + ) + + ch_multiqc_files = ch_multiqc_files.mix(RCLONE_CHECKSUM.out.combined + .flatMap { meta, check_file -> + parseRcloneCheck(meta, check_file) + } + .collectFile( + seed: "Row\tStatus\tFile\tSample\tPriority\n", + sort: false + ) { meta, checksum -> + return [ "${meta.id}_${meta.check_format}_rclone_checksum_mqc.tsv", checksum ] + } + ) // - // MODULE: Run FastQC + // MODULE: Rclone data copying // - FASTQC ( - ch_samplesheet + if(params.copy_matching_only) { + // Compute expected group size per meta.id from the input + ch_with_size = ch_checksum + .map { meta, _checksum, _hash, _source -> + [ meta.subMap(meta.keySet() - 'check_format'), 1 ] + } + .groupTuple() + .map { meta, ones -> tuple(meta, ones.size()) } + + ch_files_to_copy = RCLONE_CHECKSUM.out.match + .map { + meta, match -> [ meta.subMap(meta.keySet() - 'check_format'), match ] + } + .combine(ch_with_size, by: 0) + .map { meta, match, size -> + tuple(groupKey(meta, size), match) + } + .groupTuple() + .map { meta, files -> + def common = files + .collect { file_to_copy -> file_to_copy.readLines() } + .inject { a, b -> a.intersect(b) } + + common ? tuple(meta, common) : null + } + .filter { common -> common != null } + + CREATE_FILTER_LIST(ch_files_to_copy) + + ch_rclone_copy = ch_rclone + .join(CREATE_FILTER_LIST.out) + } else { + ch_rclone_copy = ch_rclone.map { meta, source, destination -> [ meta, source, destination, [] ] } + } + + RCLONE_COPY( + ch_rclone_copy, + ch_rclone_config, + ) + + // Wait for file copy to finish before running RCLONE_CHECK + ch_rclone_check = ch_rclone + .join(RCLONE_COPY.out.log, remainder: true) + .map { meta, input, output, _log -> [ meta, input, output ] } + + // + // File transfer validation + // + RCLONE_CHECK( + ch_rclone_check, + ch_rclone_config + ) + + ch_multiqc_files = ch_multiqc_files.mix(RCLONE_CHECK.out.combined + .flatMap { meta, check_file -> + parseRcloneCheck(meta, check_file) + } + .collectFile( + seed: "Row\tStatus\tFile\tSample\tPriority\n", + sort: false + ) { meta, check -> + return [ "${meta.id}_rclone_check_mqc.tsv", check ] + } + ) + + ch_multiqc_files = ch_multiqc_files.mix( + RCLONE_CHECK.out.exit_code + .map { meta, exit_file -> [ meta, exit_file, "CHECK" ] } + .mix(RCLONE_CHECKSUM.out.exit_code + .map { meta, exit_file -> [ meta, exit_file, "CHECKSUM_${meta.check_format.toUpperCase()}" ] } + ) + .map { meta, exit_file, module -> + createExitSummary(meta, exit_file, module) + } + .collectFile( + seed: "Row\tSample\tModule\tExit code", + sort: false, + newLine: true + ) { _meta, exit_code -> + return [ "rclone_exit_codes.tsv", exit_code ] + } ) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) // // Collate and save software versions // - softwareVersionsToYAML(ch_versions) - .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) - .set { ch_collated_versions } + def topic_versions = channel.topic("versions") + .distinct() + .branch { entry -> + versions_file: entry instanceof Path + versions_tuple: true + } + + def topic_versions_string = topic_versions.versions_tuple + .map { process, tool, version -> + [ process[process.lastIndexOf(':')+1..-1], " ${tool}: ${version}" ] + } + .groupTuple(by:0) + .map { process, tool_versions -> + tool_versions.unique().sort() + "${process}:\n${tool_versions.join('\n')}" + } + + def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + .mix(topic_versions_string) + .collectFile( + storeDir: "${outdir}/pipeline_info", + name: 'nf_core_' + 'datasync_software_' + 'mqc_' + 'versions.yml', + sort: true, + newLine: true + ) // // MODULE: MultiQC // - ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) - - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_files = ch_multiqc_files.mix(channel.fromPath(params.input).collectFile(name: 'samplesheet.csv')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + def ch_summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + def ch_workflow_summary = channel.value(paramsSummaryMultiqc(ch_summary_params)) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + def ch_multiqc_custom_methods_description = multiqc_methods_description + ? file(multiqc_methods_description, checkIfExists: true) + : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true) + def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true)) + ch_multiqc_files = ch_multiqc_files.mix(channel.value(file("${projectDir}/assets/multiqc_custom.css", checkIfExists: true))) + MULTIQC( + ch_multiqc_files.flatten().collect().map { files -> + [ + [id: 'datasync'], + files, + multiqc_config + ? file(multiqc_config, checkIfExists: true) + : file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true), + multiqc_logo ? file(multiqc_logo, checkIfExists: true) : [], + [], + [], + ] + } ) - - emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] }