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Add wipertools module (#7184) #7185

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Add wipertools module (#7184) #7185

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mazzalab
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@mazzalab mazzalab commented Dec 9, 2024 •
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New module

PR checklist

Closes #7184

  • This comment contains a description of changes (with reason).
  • 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

famosab
famosab requested changes Dec 10, 2024
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Looks good already - have some styling / convention remarks :)

modules/nf-core/wipertools/fastqgather/main.nf Outdated Show resolved Hide resolved
modules/nf-core/wipertools/fastqgather/main.nf Outdated Show resolved Hide resolved
modules/nf-core/wipertools/fastqgather/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/wipertools/fastqgather/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/wipertools/fastqgather/tests/base.config Outdated Show resolved Hide resolved
modules/nf-core/wipertools/fastqwiper/tests/main.nf.test
"""
input[0] = [
[ id:'test', single_end:true ],
file('https://raw.githubusercontent.com/nf-core/test-datasets/fastqrepair/testdata/truncated_clean.fastq', checkIfExists: true),
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update please

modules/nf-core/wipertools/reportgather/main.nf Outdated Show resolved Hide resolved
modules/nf-core/wipertools/reportgather/main.nf Outdated Show resolved Hide resolved
modules/nf-core/wipertools/reportgather/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/wipertools/reportgather/tests/main.nf.test Outdated Show resolved Hide resolved
@mazzalab mazzalab added WIP Work in progress and removed Ready for Review labels Dec 10, 2024
@mazzalab mazzalab requested a review from famosab December 10, 2024 16:13
@mazzalab mazzalab added Ready for Review and removed WIP Work in progress labels Dec 10, 2024
@mazzalab mazzalab self-assigned this Dec 10, 2024
@mazzalab mazzalab added WIP Work in progress and removed Ready for Review labels Dec 11, 2024
tm4zza
tm4zza reviewed Dec 13, 2024
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Fixed fastqscatter and fastqgather as for your suggestions. I miss fastqwiper and reportgather to complete the review from my side

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@tm4zza tm4zza tm4zza left review comments

@famosab famosab famosab requested changes

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new module: WIPERTOOLS
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@mazzalab @famosab @tm4zza @mashehu