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add skip_qualimap and skip_eklipse parameters #436

Merged
merged 4 commits into from
Oct 18, 2023
Merged

add skip_qualimap and skip_eklipse parameters #436

merged 4 commits into from
Oct 18, 2023

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ramprasadn
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@ramprasadn ramprasadn commented Oct 17, 2023 •
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PR checklist

Added an option to skip qualimap in the QC subworkflow, and eklipse in the mitochondrial sv call subworkflow.

  • 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 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>).
  • 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 Oct 17, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9b1b6c6

+| ✅ 151 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-18 10:46:29

@ramprasadn ramprasadn requested a review from jemten October 17, 2023 15:10
@ramprasadn ramprasadn marked this pull request as ready for review October 17, 2023 15:12
@ramprasadn ramprasadn changed the title add skip_qualimap parameter add skip_qualimap and skip_eklipse parameters Oct 17, 2023
marrip
marrip reviewed Oct 18, 2023
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just some small things I was a bit uncertain about :)

conf/modules/qc_bam.config Outdated
@@ -33,8 +33,10 @@ process {
ext.prefix = { "${meta.id}_hsmetrics" }
}

withName: '.*QC_BAM:QUALIMAP_BAMQC' {
ext.prefix = { "${meta.id}_qualimap" }
if (params.skip_qualimap) {
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just checking, does this need to be:

Suggested change
if (params.skip_qualimap) {
if (!params.skip_qualimap) {

as it should only run when wee are not skipping?

subworkflows/local/variant_calling/call_sv_MT.nf
eklipse_del = EKLIPSE.out.deletions // channel: [ val(meta), path(csv) ]
eklipse_genes = EKLIPSE.out.genes // channel: [ val(meta), path(csv) ]
eklipse_circos = EKLIPSE.out.circos // channel: [ val(meta), path(png) ]
eklipse_del = ch_eklipse_del // channel: [ val(meta), path(csv) ]
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will they always be empty or do I miss something here? Do you need to add the output from EKLIPSE in line 22 etc.?

@ramprasadn ramprasadn merged commit 16d6831 into nf-core:dev Oct 18, 2023
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marrip commented Oct 18, 2023

🎉

@jemten jemten deleted the skip_qualimap branch October 25, 2023 14:32
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@marrip marrip marrip approved these changes

@jemten jemten Awaiting requested review from jemten

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@ramprasadn @marrip