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Add CATPACK/CONTIGS #7334

Merged
merged 18 commits into from
Jan 21, 2025
Merged

Add CATPACK/CONTIGS #7334

merged 18 commits into from
Jan 21, 2025

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jfy133
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@jfy133 jfy133 commented Jan 19, 2025

Needs #7312 first!

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 added 15 commits January 15, 2025 14:46
@jfy133 jfy133 marked this pull request as ready for review January 20, 2025 11:26
sateeshperi
sateeshperi reviewed Jan 20, 2025
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modules/nf-core/catpack/contigs/main.nf Show resolved Hide resolved
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modules/nf-core/catpack/contigs/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/catpack/prepare/main.nf
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
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why are these changes being reverted ?

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Because $prefix is used in in the output definitons leading to test failure as they can't find them

sateeshperi
sateeshperi approved these changes Jan 20, 2025
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minor formatting suggestions...otherwise LGTM

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jfy133 commented Jan 21, 2025

Local linting is working, and this error is related to AWS runners again (Seeing it on multiple PRs) so will force merge

@jfy133 jfy133 merged commit 732e6be into nf-core:master Jan 21, 2025
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@jfy133 jfy133 deleted the catpack-cat branch January 21, 2025 07:16
This was referenced Jan 23, 2025
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@sateeshperi sateeshperi sateeshperi approved these changes

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