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update vcfanno output #7353

Merged
merged 5 commits into from
Jan 23, 2025
Merged

update vcfanno output #7353

merged 5 commits into from
Jan 23, 2025
+94 −20

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nvnieuwk
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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

jfy133
jfy133 approved these changes Jan 23, 2025
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No blockers, mostly formatting

modules/nf-core/vcfanno/main.nf Outdated
@@ -31,7 +34,8 @@ process VCFANNO {
${lua_cmd} \\
${toml} \\
${vcf} \\
> ${prefix}.vcf
| bgzip ${args2} --threads ${task.cpus} > ${prefix}.vcf.gz \\
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Split across multiple lines?

modules/nf-core/vcfanno/main.nf Show resolved Hide resolved
@nvnieuwk nvnieuwk added this pull request to the merge queue Jan 23, 2025
Merged via the queue into nf-core:master with commit b1137e2 Jan 23, 2025
22 of 24 checks passed
@nvnieuwk nvnieuwk deleted the bgzip-vcfanno branch January 23, 2025 13:39
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@jfy133 jfy133 jfy133 approved these changes

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@nvnieuwk @jfy133