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Fixed null value in publish dir #132

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Merged
maxulysse merged 1 commit into from
Feb 22, 2024
Merged

Fixed null value in publish dir #132

maxulysse merged 1 commit into from
Feb 22, 2024

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@nschcolnicov
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@nschcolnicov nschcolnicov commented Feb 21, 2024 •
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This PR is to address the issue describer here: #125

I modified the meta_map that gets fed into the GATK4 HAPLOTYPECALLER so that it contains the key "variantcaller" that is required in the VEP and SnpEff publishDir, the same way it is implemented in nf-core/sarek, in the haplotypecaller subworfklow in line 32

I tested it with a custom dataset using this command:

nextflow run ../../main.nf -profile bi,cluster --input ../input_backup.csv --outdir . --annotate_tools merge -c ../config.config -resume

The config file only contains the path to the reference data files, and the input samplesheet contains a list of samples

This ran OK:
image

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/rnavar 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 Feb 21, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit f22ec03

+| ✅ 179 tests passed       |+
!| ❗   4 tests had warnings |!
-| ❌   8 tests failed       |-
Details

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowRnavar.groovy
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in WorkflowRnavar.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-21 15:21:50

@maxulysse maxulysse merged commit 07dee64 into nf-core:dev Feb 22, 2024
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@maxulysse maxulysse maxulysse approved these changes

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@nschcolnicov @maxulysse