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Add nanoqc module #6969

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Add nanoqc module #6969

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lfreitasl
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@lfreitasl lfreitasl commented Nov 11, 2024 •
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Closes #6968

  • 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

@lfreitasl lfreitasl self-assigned this Nov 11, 2024
LeonHafner
LeonHafner reviewed Nov 14, 2024
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modules/nf-core/nanoqc/tests/main.nf.test
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match() }
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Any reason why you only check for the hashes of the versions channel and not the report and logs?

LeonHafner
LeonHafner requested changes Nov 14, 2024
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modules/nf-core/nanoqc/main.nf
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

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Suggested change

modules/nf-core/nanoqc/main.nf
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

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Suggested change

modules/nf-core/nanoqc/main.nf
$args

mv *.html ${prefix}.html
mv *.log ${prefix}.log
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Can you do it the more explicit way and match the file name directly without the globing?
Currently it looks to me like you're trying to match multiple files and rename them to the same.
Assuming the outputs are files and ${prefix}.html is no directory 😄

@LeonHafner
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Looks good overall! I've added some comments.

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@LeonHafner LeonHafner LeonHafner requested changes

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new module: NANOQC
3 participants
@lfreitasl @LeonHafner @edmundmiller