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Haplotypecaller fix + single sample germline VC#557

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maxulysse merged 27 commits intonf-core:devfrom
FriederikeHanssen:single_sample_gatk
Jun 16, 2022
Merged

Haplotypecaller fix + single sample germline VC#557
maxulysse merged 27 commits intonf-core:devfrom
FriederikeHanssen:single_sample_gatk

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@FriederikeHanssen FriederikeHanssen commented May 23, 2022

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
maxulysse reviewed Jun 9, 2022
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Comment thread subworkflows/nf-core/variantcalling/haplotypecaller/main.nf Outdated
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maxulysse commented Jun 9, 2022

@nf-core-bot fix linting

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github-actions Bot commented Jun 10, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cc5fd50

+| ✅ 144 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • 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
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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: 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-16 08:34:57

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FriederikeHanssen commented Jun 14, 2022

The test data is just no working for the single sample workflow. I always get:

  A USER ERROR has occurred: Bad input: Neither SNP nor indel resource contains variants overlapping input.  Filtering cannot be performed.

Reverse enigneering the modules test, the vcf used there was run through genotypegvcf, which is not happening in this part of the workflow

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FriederikeHanssen commented Jun 16, 2022

Alright, I don't know how to get the tests to work, last try is using the tumor reads for it. I have tested it on 17 real targeted datasets now, and it works fine.

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review June 16, 2022 08:33
maxulysse
maxulysse approved these changes Jun 16, 2022
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LGTM

@maxulysse maxulysse merged commit 6bfbdb1 into nf-core:dev Jun 16, 2022
@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 20, 2022
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