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Add skip_tools haplotypecaller_filter #889

Merged
merged 13 commits into from
Dec 12, 2022
Merged

Add skip_tools haplotypecaller_filter #889

merged 13 commits into from
Dec 12, 2022

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maxulysse
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@maxulysse maxulysse commented Dec 9, 2022 •
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close #876

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).

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github-actions bot commented Dec 9, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eae2dac

+| ✅ 150 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: cnvkit_reference

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.1
  • Run at 2022-12-11 20:03:28

@maxulysse maxulysse changed the title Add skip_tools haplotypecaller_filter cf #876 Add skip_tools haplotypecaller_filter Dec 9, 2022
@maxulysse
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Just need to add the unfiltered vcf to the csv file

@FriederikeHanssen
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Just the changelog missing, i think :)

@FriederikeHanssen FriederikeHanssen merged commit 63822b6 into nf-core:dev Dec 12, 2022
asp8200
asp8200 reviewed Dec 12, 2022
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subworkflows/local/bam_variant_calling_haplotypecaller/main.nf

main:

ch_versions = Channel.empty()
filtered_vcf = Channel.empty()
versions = Channel.empty()
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Are we in general replacing ch_versions with versions?

@maxulysse maxulysse deleted the haplotype_caller_filter_skip branch December 16, 2022 11:13
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@asp8200 asp8200 asp8200 left review comments

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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3 participants
@maxulysse @FriederikeHanssen @asp8200