Update nfcore modules in spatialaxe by khersameesh24 · Pull Request #184 · nf-core/spatialaxe

khersameesh24 · 2026-06-26T20:41:20Z

minor template v4.0.2 changes
included nf-core module Baysor - Bayor run, segfree, preview
included nf-core module Proseg - proseg, proseg2baysor
included nf-core module & subworkflow for OPT - flip, track, stat
linting fixes, changes to reduce lint warnings
data flow to channels handled
added missing meta.yml files
updated nf-test snapshot
other misc changes

closes #178

XENIUM_PATCH_STITCH failed with 'unrecognized arguments: --min-transcripts-per-cell 50'. When stitch_transcripts.py was split into xenium_patch_stitch_transcripts.py + xenium_patch_stitch_postprocess.py, the --min-transcripts-per-cell argument and its small-cell filter were dropped from the transcripts script, but conf/modules.config still injects the flag. - restore the argument + post-stitch small-cell filter (reassign transcripts of sub-threshold cells to noise, drop their polygons) - repoint tests/test_xenium_patch/test_stitch_transcripts.py from the deleted modules/.../resources/usr/bin path to bin/ (broken since the PR nf-core#154 refactor) - add TestMinTranscriptsFilter: filter behaviour, no-op control, and a subprocess CLI test reproducing the exact production invocation - remove the orphan bin/stitch_transcripts.py (superseded, unused) Validated in the module's sopa container: 15 passed.

fix(xenium_patch): restore --min-transcripts-per-cell in stitch script

heylf

Some minor comments also from me.

…fig files

heylf · 2026-08-07T08:23:38Z

@khersameesh24 please check your PR again. Probably you need to revert a lot back because we tackled now already thigns that you tried to solve. I thing what is only left is your updated for some modules.

github-actions · 2026-08-20T17:53:32Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

github-actions · 2026-08-20T17:57:07Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit de47b35

+| ✅ 284 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   6 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
schema_description - No description provided in schema for parameter: spoqc
container_configs - Could not generate container configuration files: Command 'nextflow inspect -format json /home/runner/work/spatialaxe/spatialaxe' failed: Command '['nextflow', 'inspect', '-format', 'json', '/home/runner/work/spatialaxe/spatialaxe']' returned non-zero exit status 1.

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-spatialaxe_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialaxe_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialaxe_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/pr-comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-spatialaxe_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-spatialaxe_logo_light.png
files_exist - File found: docs/images/nf-core-spatialaxe_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-spatialaxe_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowSpatialaxe.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.0.1dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.stardist_model= 2D_versatile_fluo
nextflow_config - Config default value correct: params.stardist_nuclei_model= 2D_versatile_fluo
nextflow_config - Config default value correct: params.stardist_n_tiles= 8 8
nextflow_config - Config default value correct: params.run_qc= true
nextflow_config - Config default value correct: params.cell_segmentation_only= true
nextflow_config - Config default value correct: params.expansion_distance= 5
nextflow_config - Config default value correct: params.dapi_filter= 100
nextflow_config - Config default value correct: params.interior_stain= true
nextflow_config - Config default value correct: params.boundary_stain= true
nextflow_config - Config default value correct: params.segger_accelerator= cpu
nextflow_config - Config default value correct: params.segger_knn_method= kd_tree
nextflow_config - Config default value correct: params.segger_num_workers= 4
nextflow_config - Config default value correct: params.format= xenium
nextflow_config - Config default value correct: params.baysor_scale= 30
nextflow_config - Config default value correct: params.baysor_tiling= true
nextflow_config - Config default value correct: params.baysor_tiling_micron= 1200
nextflow_config - Config default value correct: params.baysor_tiling_overlap= 200
nextflow_config - Config default value correct: params.baysor_tiling_balanced= true
nextflow_config - Config default value correct: params.baysor_tiling_scale= 39
nextflow_config - Config default value correct: params.baysor_tiling_min_mols_per_cell= 120
nextflow_config - Config default value correct: params.baysor_tiling_min_transcripts_per_cell= 50
nextflow_config - Config default value correct: params.min_transcripts_per_cell= 10
nextflow_config - Config default value correct: params.baysor_prior_confidence= 0.2
nextflow_config - Config default value correct: params.min_qv= 20.0
nextflow_config - Config default value correct: params.min_x= 0.0
nextflow_config - Config default value correct: params.max_x= 24000.0
nextflow_config - Config default value correct: params.min_y= 0.0
nextflow_config - Config default value correct: params.max_y= 24000.0
nextflow_config - Config default value correct: params.patch_grid= 3x3
nextflow_config - Config default value correct: params.patch_overlap= 50
nextflow_config - Config default value correct: params.patch_filter_iqr_multiplier= 3.0
nextflow_config - Config default value correct: params.patch_filter_z_threshold= 4.0
nextflow_config - Config default value correct: params.csplit_x_bins= 2
nextflow_config - Config default value correct: params.csplit_y_bins= 2
nextflow_config - Config default value correct: params.tile_width= 120
nextflow_config - Config default value correct: params.tile_height= 120
nextflow_config - Config default value correct: params.batch_size_train= 4
nextflow_config - Config default value correct: params.devices= 4
nextflow_config - Config default value correct: params.max_epochs= 200
nextflow_config - Config default value correct: params.batch_size_predict= 1
nextflow_config - Config default value correct: params.buffer_size= 1
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.test_data_base= https://raw.githubusercontent.com/nf-core/test-datasets/spatialaxe
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nf_test_content - 'tests/spoqc.nf.test' contains outdir parameter
nf_test_content - 'tests/spoqc.nf.test' contains outdir parameter
nf_test_content - 'tests/spoqc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/spoqc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/image_mode.nf.test' contains outdir parameter
nf_test_content - 'tests/image_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/image_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/coordinate_mode.nf.test' contains outdir parameter
nf_test_content - 'tests/coordinate_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/coordinate_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/coordinate_mode.nf.test' contains outdir parameter
nf_test_content - 'tests/coordinate_mode.nf.test' contains outdir parameter
nf_test_content - 'tests/coordinate_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/coordinate_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/segfree_mode.nf.test' contains outdir parameter
nf_test_content - 'tests/segfree_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/segfree_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/preview_mode.nf.test' contains outdir parameter
nf_test_content - 'tests/preview_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/preview_mode.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/pr-comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 26.04.6, Config: 26.04.6
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_PRE_XR_RUN found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_POST_XR_RUN found in conf/modules.config and Nextflow scripts.
modules_config - XENIUMRANGER_RELABEL found in conf/modules.config and Nextflow scripts.
modules_config - XENIUMRANGER_RESEGMENT found in conf/modules.config and Nextflow scripts.
modules_config - XENIUMRANGER_IMPORT_SEGMENTATION found in conf/modules.config and Nextflow scripts.
modules_config - PROSEG found in conf/modules.config and Nextflow scripts.
modules_config - PROSEG2BAYSOR found in conf/modules.config and Nextflow scripts.
modules_config - BAYSOR_RUN found in conf/modules.config and Nextflow scripts.
modules_config - BAYSOR_SEGFREE found in conf/modules.config and Nextflow scripts.
modules_config - BAYSOR_CREATE_DATASET found in conf/modules.config and Nextflow scripts.
modules_config - BAYSOR_PREPROCESS_TRANSCRIPTS found in conf/modules.config and Nextflow scripts.
modules_config - BAYSOR_PREVIEW found in conf/modules.config and Nextflow scripts.
modules_config - XENIUM_PATCH_DIVIDE found in conf/modules.config and Nextflow scripts.
modules_config - XENIUM_PATCH_STITCH found in conf/modules.config and Nextflow scripts.
modules_config - SEGGER_CREATE_DATASET found in conf/modules.config and Nextflow scripts.
modules_config - SEGGER_TRAIN found in conf/modules.config and Nextflow scripts.
modules_config - SEGGER_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - FICTURE_PREPROCESS found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - RESOLIFT found in conf/modules.config and Nextflow scripts.
modules_config - PARQUET2CSV found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACT_PREVIEW_DATA found in conf/modules.config and Nextflow scripts.
modules_config - GET_TRANSCRIPTS_COORDINATES found in conf/modules.config and Nextflow scripts.
modules_config - RESIZE_TIF found in conf/modules.config and Nextflow scripts.
modules_config - SEGGER2XR found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_TRANSCRIPTS found in conf/modules.config and Nextflow scripts.
modules_config - SPATIALDATA_WRITE found in conf/modules.config and Nextflow scripts.
modules_config - SPATIALDATA_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - SPATIALDATA_META found in conf/modules.config and Nextflow scripts.
modules_config - CELLPOSE found in conf/modules.config and Nextflow scripts.
modules_config - CELLPOSE_CELLS found in conf/modules.config and Nextflow scripts.
modules_config - STARDIST_NUCLEI found in conf/modules.config and Nextflow scripts.
modules_config - OPT_FLIP found in conf/modules.config and Nextflow scripts.
modules_config - OPT_TRACK found in conf/modules.config and Nextflow scripts.
modules_config - OPT_STAT found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.0.3
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 4.0.3
Run at 2026-08-20 17:56:42

github-actions · 2026-08-20T19:21:46Z

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

❌ docker | latest-everything | Shard 9/12

See the full run for details.

khersameesh24 added 6 commits June 26, 2026 14:50

fixed warning, added missing meta.yml, zenodo id

845219d

lint fix for template file

5e4c88c

added nf-core baysor module, updated baysor subworkflows

ed9764a

updated input channels, meta yml files

6d50015

added nf-core module opt, updated subworkflow

98b9aaf

added nf-core module proseg

83e3f97

khersameesh24 added the DO NOT MERGE label Jun 26, 2026

khersameesh24 added 2 commits June 26, 2026 22:47

fixed output channel for baysor preview

ee8eeeb

updated nf-test snapshot

8c5cef3

khersameesh24 changed the title ~~Update nfcore modules - placeholder PR~~ Update nfcore modules in spatialaxe Jun 27, 2026

khersameesh24 requested review from an-altosian and heylf June 27, 2026 08:55

khersameesh24 added ready for review and removed DO NOT MERGE labels Jun 27, 2026

an-altosian and others added 3 commits June 27, 2026 14:41

Merge pull request #11 from an-altosian/fix/stitch-min-transcripts-pr184

7b02685

fix(xenium_patch): restore --min-transcripts-per-cell in stitch script

restructured modules directory

394ccdc

khersameesh24 linked an issue Jun 27, 2026 that may be closed by this pull request

[update] existing nf-core modules #178

Open

mashehu reviewed Jun 29, 2026

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Comment thread .nf-core.yml

mashehu reviewed Jun 29, 2026

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heylf reviewed Jul 8, 2026

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Comment thread conf/modules.config Outdated

heylf reviewed Jul 8, 2026

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Comment thread subworkflows/local/baysor_run_transcripts_parquet/main.nf Outdated

heylf reviewed Jul 8, 2026

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Comment thread subworkflows/local/ficture_preprocess_model/main.nf Outdated

heylf reviewed Jul 8, 2026

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added module for baysor scale estimation, minor fixes, tool-based con…

aa552a3

…fig files

khersameesh24 added DO NOT MERGE and removed ready for review labels Jul 12, 2026

lint fix

0945ab2

khersameesh24 added the bug Something isn't working label Jul 12, 2026

added nf-test for estimate-scale-factor

292baeb

Merge branch 'dev' into update-nfcore-modules

de47b35

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Update nfcore modules in spatialaxe - #184

Update nfcore modules in spatialaxe#184
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khersameesh24 commented Jun 26, 2026 •

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github-actions Bot commented Aug 20, 2026

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khersameesh24 commented Jun 26, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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heylf commented Aug 7, 2026

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github-actions Bot commented Aug 20, 2026

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github-actions Bot commented Aug 20, 2026

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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github-actions Bot commented Aug 20, 2026

❌ nf-test failed with latest Nextflow version

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khersameesh24 commented Jun 26, 2026 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️