diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 945c56f..01bb137 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -20,12 +20,12 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 with: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" @@ -38,6 +38,8 @@ runs: - 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') diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index b498008..5a8075d 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -24,9 +24,6 @@ jobs: - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # 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 with: workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 172de6f..b694012 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10 + - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index a7bf4fc..ca2eb82 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -39,15 +39,15 @@ jobs: needs: configure steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" architecture: "x64" diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 8837738..8579c6f 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,12 +32,12 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 # Install and run prek - name: Run prek id: prek - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 continue-on-error: true # indication that the linting has finished diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bc32219..277f12f 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,30 +11,30 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - name: Run prek - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" architecture: "x64" - name: Setup uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 @@ -46,7 +46,7 @@ jobs: run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} + if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 4de681a..e363215 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: fetch-depth: 0 @@ -85,7 +85,7 @@ jobs: TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: fetch-depth: 0 diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index ee102f7..149e285 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.gitignore b/.gitignore index cc2b1a7..5516a06 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ testing* *.pyc null/ .lineage/ +.nf-test* diff --git a/.hooks/block_pipeline_outdir.sh b/.hooks/block_pipeline_outdir.sh new file mode 100755 index 0000000..e9ba4f9 --- /dev/null +++ b/.hooks/block_pipeline_outdir.sh @@ -0,0 +1,44 @@ +#!/usr/bin/env bash +# This hook is used to block commits if they include staged files inside a directory +# which also contains a subdirectory called `pipeline_info`. The purpose of this is to +# prevent users from inadvertently committing output from pipeline test runs inside the +# development directory. + +set -e + +status=0 +seen_dirs="" + +while IFS= read -r file; do + # The offending output bundle's root is the ancestor directory that has + # `pipeline_info` as an immediate child, so callers can restore it in one go. + if [[ "$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 d72e474..046dfb2 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,14 +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: 4.0.3 +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. + 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: 1.0dev + version: 1.0.0 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f51e1a2..e9503db 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.8.3 + - prettier@3.9.6 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -25,9 +25,26 @@ repos: 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/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 3032c6f..aaca6d9 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,13 +10,19 @@ ## 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. + > 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 diff --git a/README.md b/README.md index 3d20e4c..96f62ea 100644 --- a/README.md +++ b/README.md @@ -9,72 +9,72 @@ [![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) [![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-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3) +[![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 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 bioinformatics pipeline that ... +**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. - -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +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. -## Usage +The current tested use case for this pipeline is transfer between S3 buckets. -> [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data. +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/). - +To run the pipeline on your own data, create a samplesheet containing one transfer per row: -Now, you can run the pipeline using: +```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 +``` - +Then launch the pipeline using: ```bash nextflow run nf-core/datasync \ - -profile \ - --input samplesheet.csv \ - --outdir + -r \ + -profile docker \ + --input samplesheet.csv \ + --outdir results \ + --rclone_config /path/to/rclone.conf ``` -> [!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/docs/running/run-pipelines#using-parameter-files). +`--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. -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). +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 @@ -82,7 +82,11 @@ 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 @@ -95,8 +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/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/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 248b66e..6d286fd 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -4,6 +4,7 @@ "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?://.*$" + } + } + ], + "errorMessage": "Output path must be a local path or object-storage URI such as s3://bucket/path; HTTP(S) URLs and rclone remote:path syntax are not supported" + }, + "checksum_md5": { "type": "string", "format": "file-path", - "exists": true, - "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", - "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)$", + "errorMessage": "Checksum_md5 cannot contain spaces" }, - "fastq_2": { + "checksum_sha": { "type": "string", "format": "file-path", - "exists": true, - "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", - "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/conf/base.config b/conf/base.config index 84af848..f65f108 100644 --- a/conf/base.config +++ b/conf/base.config @@ -10,7 +10,6 @@ process { - // TODO nf-core: Check the defaults for all processes cpus = { 1 * task.attempt } memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } @@ -24,7 +23,6 @@ process { // 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 = { 1 } @@ -49,6 +47,9 @@ process { withLabel:process_long { time = { 20.h * task.attempt } } + withLabel:process_low_memory { + memory = { 1.GB * task.attempt } + } withLabel:process_high_memory { memory = { 200.GB * task.attempt } } diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config index d3ee1b4..584667d 100644 --- a/conf/containers_conda_lock_files_amd64.config +++ b/conf/containers_conda_lock_files_amd64.config @@ -1,2 +1,4 @@ -process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } } -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } } +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 index 2b90ac4..028f0ed 100644 --- a/conf/containers_conda_lock_files_arm64.config +++ b/conf/containers_conda_lock_files_arm64.config @@ -1,2 +1,4 @@ -process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } } -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } } +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 index 65f1814..79d0789 100644 --- a/conf/containers_docker_amd64.config +++ b/conf/containers_docker_amd64.config @@ -1,2 +1,4 @@ -process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2' } } -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } } +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 index 6c845ba..921367a 100644 --- a/conf/containers_docker_arm64.config +++ b/conf/containers_docker_arm64.config @@ -1,2 +1,4 @@ -process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68' } } -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } } +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 index 838f248..0c31c94 100644 --- a/conf/containers_singularity_https_amd64.config +++ b/conf/containers_singularity_https_amd64.config @@ -1,2 +1,4 @@ -process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data' } } -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } } +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 index 090173b..f480fe7 100644 --- a/conf/containers_singularity_https_arm64.config +++ b/conf/containers_singularity_https_arm64.config @@ -1,2 +1,4 @@ -process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data' } } -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } } +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 index 773f369..2cf2119 100644 --- a/conf/containers_singularity_oras_amd64.config +++ b/conf/containers_singularity_oras_amd64.config @@ -1,2 +1,4 @@ -process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd' } } -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } } +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 index 798cc63..026fe86 100644 --- a/conf/containers_singularity_oras_arm64.config +++ b/conf/containers_singularity_oras_arm64.config @@ -1,2 +1,4 @@ -process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035' } } -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } } +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/igenomes_ignored.config b/conf/igenomes_ignored.config deleted file mode 100644 index b4034d8..0000000 --- a/conf/igenomes_ignored.config +++ /dev/null @@ -1,9 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for iGenomes paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Empty genomes dictionary to use when igenomes is ignored. ----------------------------------------------------------------------------------------- -*/ - -params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index d203d2b..e13b34f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,16 +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: 'RCLONE_CHECK' { + ext.prefix = { "${meta.id}_check" } + ext.args = { + def base_args = [ + '--no-check-certificate', + '--one-way' + ] + base_args.join(' ') + } + publishDir = [ + path: { "${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 7b7af9e..f152167 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,8 +23,7 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // 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 = params.pipelines_testdata_base_path + '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 f11bc7e..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 = params.pipelines_testdata_base_path + '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 index 3e8477b..9c5bceb 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -40,12 +40,12 @@ The nf-core stance on the use of AI and LLMs is that humans are still ultimately If you’re using AI tools, try to stick by these guidelines: -- Keep PRs as small and focussed as possible +- 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 the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team. +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 @@ -128,7 +128,7 @@ Please also refer to the [pipeline-specific contribution guidelines](#pipeline-s - [ ] 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) the code with nf-core/tools. +- [ ] [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. @@ -166,7 +166,7 @@ Specify these with generic `withLabel:` selectors, so they can be shared across 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 the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). +Values assigned within these labels can be dynamically passed to a tool using the `${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 @@ -182,4 +182,4 @@ If you update images or graphics, follow the nf-core [style guidelines](https:// ## 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 List","patterns":[],"r":5.0,"region":"datasync","rx":5.0,"w":10.0,"x":236.0,"y":167.0},{"groups":["main"],"h":10.0,"id":"node3","label":"Rclone\nCheck","patterns":[],"r":5.0,"region":"datasync","rx":5.0,"w":10.0,"x":356.0,"y":200.4},{"groups":["main"],"h":10.0,"id":"node4","label":"Rclone\nCopy","patterns":[],"r":5.0,"region":"datasync","rx":5.0,"w":10.0,"x":296.0,"y":200.4},{"groups":["main"],"h":10.0,"id":"node5","label":"MultiQC","patterns":[],"r":5.0,"region":"datasync","rx":5.0,"w":10.0,"x":416.0,"y":200.4},{"groups":["main"],"h":10.0,"id":"report_out","label":"Output","patterns":[],"r":5.0,"region":"datasync","rx":5.0,"w":10.0,"x":476.0,"y":200.4}],"regions":[{"id":"datasync","label":"Datasync pipeline"}],"title":"nf-core/datasync","version":"1.0","width":594} + + +nf-core/datasync + + +1 +Datasync pipeline + + + + + + + + + + + + + + + +CSV +InputSamplesheet + + + + + + + + + +Config +RcloneConfig + + + + + + + + + + + + + + + + + + + + + + + + +HTML +Report + + + +RcloneChecksum + +CreateFilter List + +RcloneCopy + +RcloneCheck + +MultiQC + + +Pipeline +created with nf-metro v2.0.0 + diff --git a/docs/output.md b/docs/output.md index 1b7eb8b..b37a1d7 100644 --- a/docs/output.md +++ b/docs/output.md @@ -2,60 +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 (`!`). -## Pipeline overview +
    -The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: +Two integrity stages create reports: -- [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 +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//`. -### FastQC +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. -
    -Output files +The combined files use `rclone`'s one-character status prefixes: -- `fastqc/` - - `*_fastqc.html`: FastQC report containing quality metrics. - - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. +| 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. -[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/). - -### MultiQC +## MultiQC
    Output files - `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. + - `multiqc_report.html`: standalone report viewable in a browser. + - `multiqc_data/`: machine-readable data, logs, source inventory, software versions, and parsed rclone tables.
    -[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. +The MultiQC report consolidates: + +- 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. + +### Validation summary + +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. + +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). -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 . +![nf-core/multiqc validation summary](images/datasync-multiqc-exit-code-table.png) -### Pipeline information +### `rclone checksum` section (source integrity checks) + +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) + +### `rclone check` section (post-transfer checks) + +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. + +![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 1c85a3e..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. -An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. +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. + +> [!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: @@ -95,14 +227,99 @@ 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 -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: +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 pull nf-core/datasync +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 + +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 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 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. @@ -153,7 +370,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `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). + - 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. @@ -171,8 +388,19 @@ 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 pipeline steps, 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 resources request (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' + } +} +``` + +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 @@ -194,21 +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). - -## 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 637723e..d62052e 100644 --- a/main.nf +++ b/main.nf @@ -18,18 +18,6 @@ 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') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -56,6 +44,7 @@ workflow NFCORE_DATASYNC { 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 diff --git a/modules.json b/modules.json index 578acbb..ef4f2b6 100644 --- a/modules.json +++ b/modules.json @@ -5,14 +5,24 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "fastqc": { + "multiqc": { "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", "installed_by": ["modules"] }, - "multiqc": { + "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": "008f9d3e61209bf995edac3ba531f54e269e1215", + "git_sha": "0f1a09cd10bb7a05bfedb3d8780f985751f9c614", "installed_by": ["modules"] } } @@ -21,7 +31,7 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { @@ -31,7 +41,7 @@ }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57", + "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/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt deleted file mode 100644 index 7770ccd..0000000 --- a/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt +++ /dev/null @@ -1,822 +0,0 @@ - -version: 6 -environments: 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-timestamp: 1764777145593 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf deleted file mode 100644 index 1085126..0000000 --- a/modules/nf-core/fastqc/main.nf +++ /dev/null @@ -1,57 +0,0 @@ -process FASTQC { - tag "${meta.id}" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' - : 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0'}" - - input: - tuple val(meta), path(reads, stageAs: '?/*') - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip"), emit: zip - tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[reads, "${prefix}.${reads.extension}"]] : reads.withIndex().collect { entry, index -> [entry, "${prefix}_${index + 1}.${entry.extension}"] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect { _old_name, new_name -> new_name }.join(' ') - - // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) - // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 - // Dividing the task.memory by task.cpus allows to stick to requested amount of RAM in the label - def memory_in_mb = task.memory - ? (task.memory.toUnit('MB') / task.cpus).intValue() - : null - // FastQC memory value allowed range (100 - 10000) - def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) - def fastqc_memory_arg = fastqc_memory ? "--memory ${fastqc_memory}" : '' - - """ - printf "%s %s\\n" ${rename_to} | while read old_name new_name; do - [ -f "\${new_name}" ] || ln -s \$old_name \$new_name - done - - fastqc \\ - ${args} \\ - --threads ${task.cpus} \\ - ${fastqc_memory_arg} \\ - ${renamed_files} - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.html - touch ${prefix}.zip - """ -} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml deleted file mode 100644 index 2f6cfef..0000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,111 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] - identifier: biotools:fastqc -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - ontologies: [] -output: - html: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.html": - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - ontologies: [] - zip: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.zip": - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - ontologies: [] - versions_fastqc: - - - ${task.process}: - type: string - description: The process the versions were collected from - - fastqc: - type: string - description: The tool name - - fastqc --version | sed "/FastQC v/!d; s/.*v//": - type: eval - description: The expression to obtain the version of the tool - -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - fastqc: - type: string - description: The tool name - - fastqc --version | sed "/FastQC v/!d; s/.*v//": - type: eval - description: The expression to obtain the version of the tool -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -maintainers: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -containers: - docker: - linux/arm64: - name: community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68 - build_id: bd-e455e32f745abe68_1 - scan_id: sc-f102f736465af88c_1 - linux/amd64: - name: community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2 - build_id: bd-5cb1a2fa2f18c7c2_1 - scan_id: sc-0c0466326b6b77d2_1 - singularity: - linux/amd64: - name: oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd - build_id: bd-5c4bd442468d75dd_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data - linux/arm64: - name: oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035 - build_id: bd-127a87fc06499035_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data - conda: - linux/amd64: - lock_file: modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt - linux/arm64: - lock_file: modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test deleted file mode 100644 index 66c44da..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,309 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("sarscov2 single-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
    Mon 2 Oct 2023
    test.gz
    - // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 paired-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 interleaved [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 paired-end [bam]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 multiple [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 custom_prefix") { - - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } - ) - } - } - - test("sarscov2 single-end [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 paired-end [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 interleaved [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 paired-end [bam] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 multiple [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 custom_prefix - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap deleted file mode 100644 index c8ee120..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ /dev/null @@ -1,476 +0,0 @@ -{ - "sarscov2 custom_prefix": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:14.518503" - }, - "sarscov2 single-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "html": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "zip": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:19.309008" - }, - "sarscov2 custom_prefix - stub": { - "content": [ - { - "0": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "html": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ], - "zip": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:39:44.94888" - }, - "sarscov2 interleaved [fastq]": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:38:45.168496" - }, - "sarscov2 paired-end [bam]": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-28T16:38:53.268919" - }, - "sarscov2 multiple [fastq]": { - "content": [ - { - "versions_fastqc": [ - [ - "FASTQC", - "fastqc", - "0.12.1" - ] - ] - 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bioconda::multiqc=1.35 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index e80e8cd..c4bc715 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -4,8 +4,8 @@ process MULTIQC { 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/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' - : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' + : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" input: tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 2facc62..27ce18d 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -110,24 +110,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt + 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-d167b8012595a136_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt docker: linux/amd64: - name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6 - build_id: bd-db7c73dae76bc9e6_1 - scan_id: sc-66fc7138dbf1cf48_1 + 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:1.34--d167b8012595a136 - build_id: bd-d167b8012595a136_1 - scan_id: sc-ac701dfa631a2af9_1 + 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:1.34--4fc8657c816047c0 - build_id: bd-4fc8657c816047c0_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data + 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:1.34--7fbd82d945c06726 - build_id: bd-7fbd82d945c06726_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data + 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/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7c2f370..4489921 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -81,7 +81,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -175,7 +175,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -221,7 +221,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -314,7 +314,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -408,7 +408,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } 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: +pypi-prerelease-mode: if-necessary-or-explicit +packages: +linux-aarch64: +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_19.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-hf8d1292_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/rclone-1.74.3-h8f1e559_0.conda +packages: +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda +build_number: 20 +sha256: a2527b1d81792a0ccd2c05850960df119c2b6d8f5fdec97f2db7d25dc23b1068 +md5: 468fd3bb9e1f671d36c2cbc677e56f1d +depends: +- libgomp >=7.5.0 +constrains: +- openmp_impl <0.0a0 +license: BSD-3-Clause +license_family: BSD +size: 28926 +timestamp: 1770939656741 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_19.conda +sha256: 4592b096e553f67799ae70d4b6167eeda3ec74587d68c7aecbf4e7b1df136681 +md5: f35b3f52d0a2ec4ffe3c89ba135cdb9a +depends: +- _openmp_mutex >=4.5 +constrains: +- libgomp 15.2.0 h8acb6b2_19 +- libgcc-ng ==15.2.0=*_19 +license: GPL-3.0-only WITH GCC-exception-3.1 +license_family: GPL +size: 622462 +timestamp: 1778268755949 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_19.conda +sha256: 2370ef0ffcbae5bede3c4bf136add4abc257245eb91f724c99bb4a43116c5a83 +md5: c5e8a379c4a2ec2aea4ba22758c001d9 +license: GPL-3.0-only WITH GCC-exception-3.1 +license_family: GPL +size: 587387 +timestamp: 1778268674393 +- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-hf8d1292_0.conda +sha256: 369db85c5cd8d99dde364ce70725d76511d9c8199e5b820c740414091bf5bcca +md5: b2a43456aa56fe80c2477a5094899eff +depends: +- libgcc >=14 +license: 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/fastqc/environment.yml b/modules/nf-core/rclone/check/environment.yml similarity index 80% rename from modules/nf-core/fastqc/environment.yml rename to modules/nf-core/rclone/check/environment.yml index f9f54ee..ea96315 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/rclone/check/environment.yml @@ -2,6 +2,5 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - - bioconda dependencies: - - bioconda::fastqc=0.12.1 + - "conda-forge::rclone=1.74.3" diff --git a/modules/nf-core/rclone/check/main.nf b/modules/nf-core/rclone/check/main.nf new file mode 100644 index 0000000..e913b29 --- /dev/null +++ b/modules/nf-core/rclone/check/main.nf @@ -0,0 +1,94 @@ +process RCLONE_CHECK { + tag "${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 1b1ea2e..a2e4e93 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,15 +9,9 @@ // 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 - // MultiQC options multiqc_config = null multiqc_title = null @@ -25,6 +19,12 @@ params { 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' @@ -36,7 +36,7 @@ params { help_full = false show_hidden = false version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + 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 @@ -58,6 +58,8 @@ 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' profiles { debug { @@ -98,7 +100,7 @@ profiles { } arm64 { process.arch = 'arm64' - // TODO https://github.com/nf-core/modules/issues/6694 + // 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 @@ -171,6 +173,7 @@ profiles { } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } + test_copy { includeConfig 'conf/test_copy.config' } } // Load nf-core custom profiles from different institutions @@ -180,9 +183,8 @@ profiles { 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 different institutions. -// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/datasync.config" : "/dev/null" +// Load nf-core/datasync custom profiles from nf-core/configs when available. +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${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 @@ -193,9 +195,6 @@ podman.registry = 'quay.io' singularity.registry = 'quay.io' charliecloud.registry = 'quay.io' -// Load igenomes.config if required -includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' - // 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. @@ -240,13 +239,52 @@ dag { manifest { name = 'nf-core/datasync' contributors = [ - // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ name: 'Alexander Peltzer', affiliation: '', email: '', github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + 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: '' ], ] @@ -255,18 +293,15 @@ manifest { mainScript = 'main.nf' defaultBranch = 'main' nextflowVersion = '!>=25.10.4' - version = '1.0dev' + version = '1.0.0' doi = '' } // Nextflow plugins plugins { - id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.7.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { - defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index 10b92c1..a4a5f43 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -40,44 +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." }, - "igenomes_base": { - "type": "string", - "description": "The base path to the igenomes reference files", - "fa_icon": "fas fa-ban", - "hidden": true, - "default": "s3://ngi-igenomes/igenomes/" + "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." } } }, @@ -208,7 +196,7 @@ "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/", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/datasync/", "hidden": true }, "trace_report_suffix": { @@ -236,9 +224,6 @@ { "$ref": "#/$defs/input_output_options" }, - { - "$ref": "#/$defs/reference_genome_options" - }, { "$ref": "#/$defs/institutional_config_options" }, diff --git a/nf-test.config b/nf-test.config index f7aaeb4..c0c14da 100644 --- a/nf-test.config +++ b/nf-test.config @@ -34,5 +34,6 @@ config { // load the necessary plugins plugins { load "nft-utils@0.0.3" + load "nft-csv@0.1.0" } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 29e366a..919556e 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2026-07-24T12:35:36+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-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)\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 bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/datasync \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> 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/docs/running/run-pipelines#using-parameter-files).\n\nFor 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).\n\n## Pipeline output\n\nTo 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.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/datasync/output).\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\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\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", + "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" @@ -31,6 +31,9 @@ { "@id": "assets/" }, + { + "@id": "bin/" + }, { "@id": "conf/" }, @@ -99,7 +102,7 @@ }, "mentions": [ { - "@id": "#48344b18-cfae-44a4-ad69-b23734224749" + "@id": "#77ce8e20-3bfe-48e3-a2ef-1e81d74d71b6" } ], "name": "nf-core/datasync" @@ -121,26 +124,48 @@ }, { "@id": "main.nf", - "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], "contributor": [ { - "@id": "https://orcid.org/0000-0002-6503-2180" + "@id": "#be129ed0-c83e-444b-85dd-6db2c42dc277" + }, + { + "@id": "#b293152b-1358-4678-a5a5-8603ccb89cd0" + }, + { + "@id": "#6e1f504a-fae3-4fca-a7b7-8d84fff28bbd" } ], "dateCreated": "", - "dateModified": "2026-07-24T12:35:36Z", + "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"], + "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/dev/"], - "version": ["1.0dev"] + "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", @@ -155,11 +180,11 @@ "version": "!>=25.10.4" }, { - "@id": "#48344b18-cfae-44a4-ad69-b23734224749", + "@id": "#77ce8e20-3bfe-48e3-a2ef-1e81d74d71b6", "@type": "TestSuite", "instance": [ { - "@id": "#867a3285-b1be-4cd0-8b71-8341c5d037f8" + "@id": "#c23bf1c1-9211-4368-a804-064620c06a63" } ], "mainEntity": { @@ -168,7 +193,7 @@ "name": "Test suite for nf-core/datasync" }, { - "@id": "#867a3285-b1be-4cd0-8b71-8341c5d037f8", + "@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", @@ -190,6 +215,11 @@ "@type": "Dataset", "description": "Additional files" }, + { + "@id": "bin/", + "@type": "Dataset", + "description": "Scripts that must be callable from a pipeline process" + }, { "@id": "conf/", "@type": "Dataset", @@ -301,6 +331,35 @@ "@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 e9e92f3..965bc4c 100644 --- a/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf @@ -88,7 +88,8 @@ workflow PIPELINE_INITIALISATION { show_hidden, before_text, after_text, - command + command, + null ) // @@ -109,22 +110,6 @@ workflow PIPELINE_INITIALISATION { channel .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json")) - .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 { samplesheet -> - validateInputSamplesheet(samplesheet) - } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } .set { ch_samplesheet } emit: @@ -183,62 +168,117 @@ workflow PIPELINE_COMPLETION { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // -// Check and validate pipeline parameters +// Prepare samplesheet channels for rclone operations // -def validateInputParameters() { - genomeExistsError() +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 ] + } } // -// Validate channels from input samplesheet +// Check and validate pipeline parameters // -def validateInputSamplesheet(input) { - def (metas, fastqs) = input[1..2] +def validateInputParameters() { - // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ meta -> meta.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+.-]*:.*/) + } + + 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!" + ) } - return [ metas[0], fastqs ] + 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 + } } + // -// Get attribute from genome config file e.g. fasta +// Create exit code summary // -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 ] - } - } - return null +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${code}"] } - // -// Exit pipeline if incorrect --genome key provided +// Parse Rclone check and checksum combined.txt file // -def genomeExistsError() { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - error(error_string) - } +def parseRcloneCheck(meta, check_file) { + def status_map = [ + '=': 'Match', + '-': 'Missing in source', + '+': 'Missing in destination', + '*': 'Mismatch', + '!': 'Error' + ] + def priority_map = [ + '!': 0, + '*': 1, + '-': 2, + '+': 3, + '=': 4 + ] + + return check_file.readLines() + .findAll { line -> line.trim() } + .collect { line -> + def fields = line.split(/ /, 2) + def status = status_map.get(fields[0], fields[0]) + def priority = priority_map.get(fields[0], 0) + + [ meta, "${meta.id}:${fields[1]}\t${status}\t${fields[1]}\t${meta.id}\t${priority}\n" ] + } } + // // 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() @@ -246,12 +286,9 @@ 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 @@ -275,15 +312,14 @@ def methodsDescriptionText(mqc_methods_yaml) { } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" - 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.
    • " + 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 d6e593e..37939ac 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -73,11 +73,23 @@ def getWorkflowVersion() { 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(), ".${filename}") - def jsonStr = groovy.json.JsonOutput.toJson(params) + def temp_pf = workflow.launchDir.resolve(".${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) - - nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + 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() } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 1df8b76..9ff0681 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -22,6 +22,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { 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: @@ -34,11 +35,11 @@ workflow UTILS_NFSCHEMA_PLUGIN { fullHelp: help_full, ] if(parameters_schema) { - help_options << [parametersSchema: parameters_schema] + help_options << [parameters_schema: parameters_schema] } log.info paramsHelp( help_options, - (params.help instanceof String && params.help != "true") ? params.help : "", + (help instanceof String && help != "true") ? help : "", ) exit 0 } @@ -50,7 +51,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { summary_options = [:] if(parameters_schema) { - summary_options << [parametersSchema: parameters_schema] + summary_options << [parameters_schema: parameters_schema] } log.info before_text log.info paramsSummaryLog(summary_options, input_workflow) @@ -63,7 +64,10 @@ workflow UTILS_NFSCHEMA_PLUGIN { if(validate_params) { validateOptions = [:] if(parameters_schema) { - validateOptions << [parametersSchema: parameters_schema] + validateOptions << [parameters_schema: parameters_schema] + } + if(cli_typecast != null) { + validateOptions << [cast_cli_params: cli_typecast] } validateParameters(validateOptions) } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml index f7d9f02..1d8c75a 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -25,6 +25,30 @@ input: 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 diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index c977917..1fd1eac 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -31,6 +31,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -63,6 +64,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -95,6 +97,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -127,6 +130,7 @@ nextflow_workflow { input[6] = "" input[7] = "" input[8] = "" + input[9] = null """ } } @@ -160,6 +164,7 @@ nextflow_workflow { input[6] = "Before" input[7] = "After" input[8] = "nextflow run test/test" + input[9] = null """ } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index f6537cc..fd71cb8 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.6.1" + id "nf-schema@2.7.2" } validation { diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 331e0d2..e1fa4e2 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "$id": "https://raw.githubusercontent.com/./main/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", diff --git a/tests/.nftignore b/tests/.nftignore index e128a12..b1e73cd 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -10,3 +10,4 @@ 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 index 7576e53..0178b64 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test pipeline" script "../main.nf" tag "pipeline" + profile "test" test("-profile test") { @@ -17,15 +18,20 @@ nextflow_pipeline { def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_content: All files in ${params.outdir}/ with stable content def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - assert workflow.success + // Summarise rclone outputs by line count + def rclone_reports = getAllFilesFromDir(params.outdir, relative: true, include: ['rclone/**/*.txt']) + def rclone_line_counts = rclone_reports.findAll { !it.endsWith('.exit_code.txt') }.collect { file -> "${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 + 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 index da48321..b912e04 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,11 +4,11 @@ ======================================================================================== */ -// TODO nf-core: Specify any additional parameters here // 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/refs/heads/datasync/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/datasync/' } -aws.client.anonymous = true // fixes S3 access issues on self-hosted runners +// Fixes S3 access issues on self-hosted runners +aws.client.anonymous = true diff --git a/workflows/datasync.nf b/workflows/datasync.nf index 7d12501..cb7a6d9 100644 --- a/workflows/datasync.nf +++ b/workflows/datasync.nf @@ -3,12 +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-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 { 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' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -24,16 +30,133 @@ workflow DATASYNC { multiqc_logo multiqc_methods_description outdir + rclone_config main: - def ch_versions = channel.empty() - def 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) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.map{ _meta, file -> file }) + 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 ] + } + ) // // Collate and save software versions @@ -67,6 +190,7 @@ workflow DATASYNC { // // MODULE: MultiQC // + 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)) @@ -76,6 +200,7 @@ workflow DATASYNC { : 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 -> [