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Subsitute samtools/bam2fq with samtools/fastq #274

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merged 8 commits into from
Apr 18, 2023
Merged

Subsitute samtools/bam2fq with samtools/fastq #274

merged 8 commits into from
Apr 18, 2023

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sofstam
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@sofstam sofstam commented Mar 23, 2023

This PR closes #257

PR checklist

  • 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 pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Mar 23, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c47b9e5

+| ✅ 156 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_lint - Schema 'description' should be 'Taxonomic classification and profiling of shotgun metagenomic data'
    Found: 'Taxonomic profiling of shotgun metagenomic data'

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-04-04 16:03:28

@sofstam sofstam marked this pull request as ready for review March 29, 2023 13:39
@sofstam sofstam requested a review from a team March 30, 2023 10:16
Midnighter
Midnighter approved these changes Mar 30, 2023
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Great, thanks for making this change 🙂 Two small questions but they're not blockers.

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jfy133
jfy133 approved these changes Apr 4, 2023
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One last suggestion of a change to the emitted files but otherwise LGTM

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subworkflows/local/longread_hostremoval.nf Outdated
@@ -54,7 +54,7 @@ workflow LONGREAD_HOSTREMOVAL {

emit:
stats = SAMTOOLS_STATS.out.stats //channel: [val(meta), [reads ] ]
reads = SAMTOOLS_BAM2FQ.out.reads // channel: [ val(meta), [ reads ] ]
reads = SAMTOOLS_FASTQ.out.other // channel: [ val(meta), [ reads ] ]
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Not that we use these files anywhere else, I think it would be safer to mix all of teh outputs from FASTQ, not just other? This would have the same behavior as the old module - otherwise here you might lose of the other reads I think (depending on how samtools fastq interprets the input, no?)

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Do you suggest that we have

reads = SAMTOOLS_FASTQ.out.fastq?

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I think actually .out.fastq).mix(<module>.out.other)

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I see, that makes sense because samtools/bam2fq had one emit with all reads.
I will test and update the PR.

@jfy133 jfy133 linked an issue Apr 15, 2023 that may be closed by this pull request
Replace samtools/bam2fq with samtools/fastq #257
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sofstam commented Apr 17, 2023

I will merge this PR.

@sofstam sofstam merged commit 255b492 into nf-core:dev Apr 18, 2023
@sofstam sofstam deleted the samtools_fastq branch April 18, 2023 14:28
@sofstam sofstam mentioned this pull request Apr 18, 2023
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@Midnighter Midnighter Midnighter approved these changes

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Replace samtools/bam2fq with samtools/fastq
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@sofstam @Midnighter @jfy133