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Added fastq_bwa_mem_samblaster #5582

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Added fastq_bwa_mem_samblaster #5582

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GallVp
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@GallVp GallVp commented May 9, 2024

PR checklist

Closes #4909

  • Added fastq_bwa_mem_samblaster
  • 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

@GallVp GallVp requested a review from a team as a code owner May 9, 2024 21:32
@GallVp GallVp requested review from adamrtalbot and removed request for a team May 9, 2024 21:32
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Do you know if samblaster works on CRAM files?

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GallVp commented Jul 29, 2024

Do you know if samblaster works on CRAM files?

According to this the developer has no plans to support CRAM for now: GregoryFaust/samblaster#25 (comment)

SPPearce
SPPearce reviewed Aug 27, 2024
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Can we swap to the . notation that the other subworkflows generally use?

subworkflows/nf-core/fastq_bwa_mem_samblaster/tests/nextflow.config
@@ -0,0 +1,11 @@
process {
withName: BWA_MEM {
ext.prefix = { "${meta.id}.on.${meta.ref_id}.bwa.mem" }
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Why these prefixes?

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Although these prefixes are not necessary here but in a pipeline they are as fastqs from each sample are mapped to each reference.

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GallVp commented Aug 27, 2024

Can we swap to the . notation that the other subworkflows generally use?

Thank you for the review.

Do you mean swapping | with .? Yes, I have no objection to that other than that I prefer | as it is visually more explicit compared to a small .

@GallVp GallVp force-pushed the fastq_bwa_mem_samblaster branch from 8b53fe0 to dca715d Compare August 27, 2024 21:38
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GallVp commented Nov 24, 2024

Closing this as it has not gained any interest from any other pipeline. If someone comes looking for this or something similar, please find it here: https://github.com/GallVp/nxf-components/blob/c30c8320078c68e14e41516ec6eaaca5f084ef38/subworkflows/gallvp/fastq_bwa_mem_samblaster/main.nf#L5

@GallVp GallVp closed this Nov 24, 2024
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@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot adamrtalbot was automatically assigned from nf-core/nf-test

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new subworkflow: FASTQ_BWA_MEM_SAMBLASTER
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