Skip to content

Replace several skip parameters with a skip_subworkflows parameter #694

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
merged 16 commits into from
Apr 14, 2025
Merged

Replace several skip parameters with a skip_subworkflows parameter #694

merged 16 commits into from
Apr 14, 2025

Conversation

ramprasadn
Copy link
Collaborator

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@github-actions GitHub Actions
Copy link

github-actions bot commented Mar 30, 2025 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3928781

+| ✅ 202 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • schema_lint - Input mimetype is missing or empty
  • local_component_structure - align.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - generate_cytosure_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - generate_clinical_set.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - qc_bam.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - variant_evaluation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_repeat_expansions.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_references.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_mt_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_repeat_expansions.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_genome_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - gens.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_snv.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_consequence_pli.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - rank_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - scatter_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - subsample_mt.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-04-14 08:39:31

@ramprasadn ramprasadn marked this pull request as ready for review April 14, 2025 08:38
kubranarci
kubranarci approved these changes Apr 14, 2025
View reviewed changes
Copy link

@kubranarci kubranarci left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I like the new way of input parameterization :D

workflows/raredisease.nf
ch_genome_dictionary,
ch_genome_fai,
ch_genome_fasta
).split_intervals
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

.out.split_intervals ?

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

.out part is not necessary when its part of invocation. But if we want to access SCATTER_GENOME's output elsewhere, then we need to use .out.

Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I see, thanks for the clarification!

workflows/raredisease.nf
@@ -413,7 +414,7 @@ workflow RAREDISEASE {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

if (!params.skip_repeat_calling && params.analysis_type.equals("wgs") ) {
if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('repeat_calling')) && params.analysis_type.equals("wgs") ) {
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

why repeat expansion is only possible for wgs? might not be ideal but can be run with wes

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Tools used here have been a bit flaky with wes samples. I could add an override in future, like I do with "run_mt_for_wes" parameter so users can choose to turn on this workflow for wes samples. Will do that in a different PR.

@ramprasadn ramprasadn merged commit d87e6e4 into dev Apr 14, 2025
12 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@kubranarci kubranarci kubranarci approved these changes

@rannick rannick Awaiting requested review from rannick

@jemten jemten Awaiting requested review from jemten

@fellen31 fellen31 Awaiting requested review from fellen31

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@ramprasadn @kubranarci