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Added missing defs #130

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Merged
maxulysse merged 4 commits into from
Feb 20, 2024
Merged

Added missing defs #130

maxulysse merged 4 commits into from
Feb 20, 2024

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@nschcolnicov
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@nschcolnicov nschcolnicov commented Feb 20, 2024 •
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This is the fix for this issue: #128
It was simply a missing "def" when defining a meta.clone() which was messing up the samples

I tested it by running:
nextflow run nschcolnicov/rnavar -r fix_multi_sample -latest -profile bi,cluster --outdir . --annotate_tools merge --input https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet_full.csv -c ../config.config -resume

image

And I also ran:
nextflow run nschcolnicov/rnavar -r fix_multi_sample -latest -profile bi,cluster --outdir . --annotate_tools vep --input https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet_full.csv -c ../config.config -resume

image

The file that was causing the issue was subworkflows/local/splitncigar/main.nf, but I also updated the local variables in rnavar.nf to avoid having issues in the future. I also spotted that there is a subworkflow from nf-core that is being used by this pipeline that is also missing some "def" in their local variable definition, but I will have to modify the nf-core/modules first. This subworkflow is not causing any issues regardless.

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 20, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 80f755c

+| ✅ 188 tests passed       |+
!| ❗   4 tests had warnings |!
Details

❗ 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 2.12.1
  • Run at 2024-02-20 15:27:24

maxulysse
maxulysse reviewed Feb 20, 2024
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@nschcolnicov @maxulysse
Update CHANGELOG.md
80f755c 
Co-authored-by: Maxime U Garcia <[email protected]>
@maxulysse maxulysse merged commit 9036f17 into nf-core:dev Feb 20, 2024
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