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Replace nfcore modules #478

Merged
merged 31 commits into from
Jan 5, 2022
Merged

Replace nfcore modules #478

merged 31 commits into from
Jan 5, 2022

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FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Dec 29, 2021 •
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  • gatk4/applybqsr
  • gatk4/baserecalibrator
  • gatk4/estimatelibrarycomplexity
  • gatk4/gatherbqsrreports
  • gatk4/genotypegvcfs
  • gatk4/haplotypecallers
  • gatk4/markduplicates
  • gatk4/mutect2

update:

  • gatk4/createsequencedictionary

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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).
  • 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 29, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7f8a537

+| ✅ 135 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2021-12-29 15:43:56

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review January 5, 2022 09:41
marissaDubbelaar
marissaDubbelaar approved these changes Jan 5, 2022
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LGTM

@FriederikeHanssen FriederikeHanssen merged commit d73a192 into nf-core:dev Jan 5, 2022
@FriederikeHanssen FriederikeHanssen deleted the replace_nfcore_modules branch July 10, 2023 18:59
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@marissaDubbelaar marissaDubbelaar marissaDubbelaar approved these changes

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

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@FriederikeHanssen @marissaDubbelaar