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Adding peak-calling with Genrich (fix #108) and multi-mapping read analysis #331

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Adding peak-calling with Genrich (fix #108) and multi-mapping read analysis #331

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samuelruizperez
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@samuelruizperez samuelruizperez commented Aug 22, 2023 •
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This PR:

  1. Addresses issue Addition of peak-calling with Genrich #108:

    This version of the pipeline keeps the current pipeline structure the same but adds a separate "branch" for peak-calling with Genrich and its necessary up and downstream processes.

    NOTES:

  1. Adds a parameter --analyze_multimappers <Int> to include multimapping reads (secondary alignments) in Genrich's peak calling process (see Genrich#multimap). Currently, it only works with --aligner bowtie2 or --aligner star, the option with Chromap is a work in progress.

    For example, setting --analyze_multimappers 50, will run Bowtie2 with -k 50 (or STAR with --outFilterMultimapNmax 50 --winAnchorMultimapNmax 100) and Genrich with -s 50. This means the aligner will report 50 distinct valid alignments for each read, and Genrich will keep secondary alignments whose scores are within 50 of the best for peak calling.

    Secondary alignments will still be filtered out with samtools view -q 1 -F 4 -F 256 before calling peaks with MACS2 unless --keep_multi_map is set.

    NOTES:

    • I have tested --analyze_multimappers with all the test datasets without issues, but when using other experimental data I have found that the allocated resources for Bowtie2 alignment (withLabel:process_high) might not be enough. Usually, it runs out of time or memory. Perhaps we could set up a conditional label/process resource allocation when this parameter is used with Bowtie2?

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • 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).

I would really appreciate it if you could take a look at these changes. This is my first attempt at a contribution to nf-core, so please let me know if have made any basic mistakes or if I could do something better to follow the guidelines.

Thanks!

@samuelruizperez

@samuelruizperez samuelruizperez added enhancement New feature or request WIP Work in progress labels Aug 22, 2023
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github-actions bot commented Aug 22, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3f103dd

+| ✅ 156 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 22]
  • system_exit - System.exit in WorkflowAtacseq.groovy: System.exit(1) [line 35]

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-08 13:01:36

@samuelruizperez samuelruizperez added this to the 2.2 milestone Aug 23, 2023
@JoseEspinosa JoseEspinosa mentioned this pull request Oct 16, 2023
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@lpantano
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Hi, I am interesting in this PR, I am happy to catch up and make it happens. Just want to make sure is ok for me to take this, or work with somebody to get it done.

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