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Replace several skip_<tools> parameters with a single skip_tools parameter #690

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Merged
merged 12 commits into from
Mar 26, 2025
Merged

Replace several skip_<tools> parameters with a single skip_tools parameter #690

merged 12 commits into from
Mar 26, 2025

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@ramprasadn
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@ramprasadn ramprasadn commented Mar 24, 2025

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).

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github-actions bot commented Mar 24, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cc9ca05

+| ✅ 203 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  20 tests had warnings |!

❗ Test warnings:

  • 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 2025-03-24 17:23:37

@ramprasadn ramprasadn marked this pull request as ready for review March 25, 2025 08:10
kubranarci
kubranarci reviewed Mar 25, 2025
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nextflow.config
skip_repeat_annotation = false
skip_repeat_calling = false
skip_smncopynumbercaller = false
skip_snv_annotation = false
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@kubranarci kubranarci Mar 25, 2025

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are you planning to add another skip parameter for the remaining params? Or you plan to infer it from samplesheet in future?

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@ramprasadn ramprasadn Mar 25, 2025

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Other skip parameters turn off entire subworkflows so it would be misleading to combine them under skip_tools. So as of now, I don't plan on combining them with skip_tools:)

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himm, maybe having them combine into --skip_subworkflows, or adding like --steps "snvcalling, snvannotation,repeat_annotation" might work.. I guess I am into clustering :)

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@ramprasadn ramprasadn Mar 26, 2025

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That's a good idea. I will do that in a different PR.

nextflow_schema.json
"description": "Specifies whether or not to skip smncopynumbercaller.",
"fa_icon": "fas fa-toggle-on"
},
"skip_snv_annotation": {
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might make sense to add more general skip option here? like skip "annotation"? I think it would be a rare case to have lets say snvannotation on while svannotaton off?

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@ramprasadn ramprasadn Mar 25, 2025

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Depends on the use case, I believe. There are scenarios where someone might have updated databases for SNVs, and in such cases, they might not want to run SV annotation.

CHANGELOG.md
| skip_germlinecnvcaller | |
| skip_peddy | |
| skip_smncopynumbercaller | |
| skip_vcf2cytosure | |
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@kubranarci kubranarci Mar 25, 2025

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add skip_fastqc

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@ramprasadn ramprasadn Mar 25, 2025

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skip_fastqc doesn't exist actually. I just added that functionality to skip_tools 😅

kubranarci
kubranarci approved these changes Mar 25, 2025
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LGTM :)

@ramprasadn ramprasadn merged commit a0560a4 into dev Mar 26, 2025
16 checks passed
@ramprasadn ramprasadn deleted the skip_tools branch March 27, 2025 07:33
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@kubranarci kubranarci kubranarci approved these changes

@jemten jemten Awaiting requested review from jemten

@fellen31 fellen31 Awaiting requested review from fellen31

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@ramprasadn @kubranarci