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Fix SVDB/merge stubs #6787

Merged
merged 2 commits into from
Oct 16, 2024
Merged

Fix SVDB/merge stubs #6787

merged 2 commits into from
Oct 16, 2024

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fellen31
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PR checklist

Closes #XXX

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@fellen31 fellen31 marked this pull request as ready for review October 16, 2024 09:47
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@Lucpen Lucpen left a comment

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Just one tiny thing

modules/nf-core/svdb/merge/main.nf Show resolved Hide resolved
@@ -48,7 +51,7 @@ process SVDB_MERGE {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
echo | gzip > ${prefix}.vcf.gz
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why not just touch the file?

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@fellen31 fellen31 Oct 16, 2024

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1.12.4 Stub gzip files must use echo and pipe in https://nf-co.re/docs/guidelines/components/modules

Simply touching a file with the file name ending in .gz will break nf-test’s Gzip file parser, as the file is not actually gzipped and thus cannot be read.

Therefore we must make sure we generate a valid gzipped file for nf-test to accept it during tests.

@fellen31 fellen31 added this pull request to the merge queue Oct 16, 2024
Merged via the queue into nf-core:master with commit 847683c Oct 16, 2024
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@fellen31 fellen31 deleted the fix-svdb-merge branch October 16, 2024 11:34
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2 participants