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Replace Bowtie2 custom modules with official nf-core ones #754

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Replace Bowtie2 custom modules with official nf-core ones #754

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@jfy133 jfy133 commented Jan 24, 2025 •
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To hopefully close #694

TODOs:

  • Finish converting ASSEMBLY_ALIGN
  • Test iGenomes for host removal alternative
  • Compare outputs of dev versus this PR
  • Consider deprecating or adding extra module for generating read_ids.txt stats

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/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 Jan 24, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e17cf94

+| ✅ 329 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  52 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-13 13:13:35

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.1.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@jfy133 jfy133 mentioned this pull request Feb 5, 2025
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jfy133 commented Feb 6, 2025

@nf-core-bot fix linting

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jfy133 commented Feb 27, 2025
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jfy133 commented Feb 27, 2025 •
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Next steps (as it's been a while since I worked on this):

  • Run dev vs bowtie2fixes
    • nextflow run ../main.nf -profile test,docker --outdir ./results-bowtie2fixes
    • nextflow run nf-core/mag -r dev -profile test,docker --outdir ./results-dev
  • Compare outputs:
    • Log files
    • Output files
    • Numbers approximately same (e.g. in logs, MultiQC)
  • Run with host genome removal (check numbers))
  • Run with selecting host_genome from iGenomes to make sure that is accepted by the new modules (check numbers)
  • Check aDNA special bowtie2 assembly alignment parmaeters work
  • Check all --save_*_reads works
  • Check @MeriamOs 's issue actually fixed
  • Add extra local module for generating *.read_ids.txt stats from BOWTIE2_REMOVAL_ALIGN
  • Delete old local bowtie2 modules

To invesigate before merge

  • Test profile results in missing half expected bins (19) in this branch (9), seems to be MetaBAT
    • The depths file looks like it shows that for bowtie2fixes results that it only was calculated based on mapping against MEGAHIT-test_minigut-test_minigut_sample2.bam and not itself
    • The test profile should be mapping against own so I think somehow the join/combine combination isn't working in BINNING_PREPARATION -> I started dumping everything in the group mapping mode section

@jfy133 jfy133 mentioned this pull request Mar 13, 2025
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