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Ascat fix #1462

Merged
merged 2 commits into from
Apr 12, 2024
Merged

Ascat fix #1462

merged 2 commits into from
Apr 12, 2024

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maxulysse
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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/sarek 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>).
  • 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).

@maxulysse maxulysse marked this pull request as ready for review April 12, 2024 16:39
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github-actions bot commented Apr 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6001f7b

+| ✅ 181 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ 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: conf/modules.config
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-12 16:41:14

asp8200
asp8200 reviewed Apr 12, 2024
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subworkflows/local/bam_variant_calling_somatic_all/main.nf
@@ -60,7 +60,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
allele_files,
loci_files,
(wes ? intervals_bed_combined : []), // No intervals needed if not WES
fasta,
fasta.map{ meta, fasta -> [ fasta ] },
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Not super important right now, but shouldn't this be fixed in BAM_VARIANT_CALLING_SOMATIC_ASCAT instead?

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I'd rather we fix that in there actually

asp8200
asp8200 approved these changes Apr 12, 2024
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I'll test this as part of the full-test on dev-Sarek before release.

@maxulysse maxulysse merged commit 3c70f34 into nf-core:dev Apr 12, 2024
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@asp8200 asp8200 asp8200 approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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@maxulysse @asp8200