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Add subworkflows #479

Merged
merged 113 commits into from
Feb 11, 2022
Merged

Add subworkflows #479

merged 113 commits into from
Feb 11, 2022

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FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Jan 10, 2022 •
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  • Add UMI Subworkflow + subworkflow for bam2fastq
  • Update GATK4 modules to add another Log4j update
  • Add and update modules for variantcalling
  • Add nf-core/gatk4_subworkflows for joint_germline & mutect2 ( need updates to new syntax upstream)
  • Add/update local subworkflows for:
    • joint_germline_variant_calling
    • tumor_only_variant_calling
    • somatic_variant_calling
  • Re-institute prepare_recalibration test
  • Fix bug to mitigate stalling after mapping. Now the workflow advances if all reads of one sample have been mapped

Closes #406 #445 #403 #392 #357

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).

@maxulysse
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is this a duplicate of #476 ?

@FriederikeHanssen
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yes, am closing 476, because merging the updates was to painful

@FriederikeHanssen
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The bam2fq module is not handling the files from the UMI tests well and doesn't recognise that they are paired. using collate beforehand fixes this but requires an upstream fix of the module.

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github-actions bot commented Jan 14, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 39f7ca6

+| ✅ 135 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   7 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
  • schema_description - No description provided in schema for parameter: umi_read_structure
  • schema_description - No description provided in schema for parameter: group_by_umi_strategy

❔ 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 2022-01-18 12:04:38

@FriederikeHanssen
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The bam2fq module is not handling the files from the UMI tests well and doesn't recognise that they are paired. using collate beforehand fixes this but requires an upstream fix of the module.

Ok, so instead of using the bam2fastq modules directly, I have written a subworkflow bam2fastq.nf now that is doing the same thing as the pipeline github.com/qbic-pipelines/bamtofastq . This should make sure that files end up being properly paired

nickhsmith
nickhsmith reviewed Feb 10, 2022
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nickhsmith
nickhsmith reviewed Feb 10, 2022
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maxulysse
maxulysse approved these changes Feb 11, 2022
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<3

@maxulysse maxulysse merged commit 93e437d into nf-core:dev Feb 11, 2022
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Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install markdownlint-cli
  • Fix the markdown errors
    • Automatically: markdownlint . --fix
    • Manually resolve anything left from markdownlint .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@FriederikeHanssen FriederikeHanssen mentioned this pull request Feb 11, 2022
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@FriederikeHanssen FriederikeHanssen deleted the add_nfcore_subworkflows branch July 10, 2023 18:59
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@FriederikeHanssen @maxulysse @nickhsmith