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Published 20 hours ago • verified publisher icon nf-core

Add FASTQ_ALIGN_DNA subworkflow

Open maxulysse opened this issue 1 year ago • 8 comments

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/sarek 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).

maxulysse avatar Oct 13 '22 06:10 maxulysse

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 7ea759c

+| ✅ 154 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • 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

:grey_question: Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-10-14 17:39:13

github-actions[bot] avatar Oct 13 '22 06:10 github-actions[bot]

For the moment, neither snapaligner nor bowtie2 can be used because I haven't add them in our params.aligner

maxulysse avatar Oct 13 '22 06:10 maxulysse

cfr snapaligner It's able to handle both, but you can disable it with settings. Splitting fastq's is not an issue, but that's of course a bad idea if you want to use the included duplicate marking.

our current config looks like this

    // -b-    : Don't lock threads to cpu cores, improves performance when scheduling multiple jobs/node
    // -sm 10 : Allow 10GB of memory for sorting threads

    withName: SNAP_ALIGN {
        cpus   = { check_max( meta.tag && meta.tag == "WGS" ? 36 : 18 , "cpus" ) }
        memory = { check_max( meta.tag && meta.tag == "WGS" ? 252.GB : 126.GB , "memory" ) }
        ext.when = {params.aligner == "snapaligner"}
        ext.args = {[
            "-so",
            "-b-",
            "-sm 10",
            meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.collect{ "$it.key:$it.value" }.join("\\t") + "\"" : ""
        ].join(" ").trim()}
        publishDir = [ enabled: false ]
    }

matthdsm avatar Oct 13 '22 06:10 matthdsm

For the moment, neither snapaligner nor bowtie2 can be used because I haven't add them in our params.aligner

Probably late to the party, but have to say not a big fan of having dead code in the pipeline, it makes the whole thing less readable imo. Maybe let's discuss this later today

FriederikeHanssen avatar Oct 13 '22 06:10 FriederikeHanssen

For the moment, neither snapaligner nor bowtie2 can be used because I haven't add them in our params.aligner

Probably late to the party, but have to say not a big fan of having dead code in the pipeline, it makes the whole thing less readable imo. Maybe let's discuss this later today

Not dead code, but a placeholder for future features

maxulysse avatar Oct 13 '22 06:10 maxulysse

Also, there's no index for snap in iGenomes! hint hint @FriederikeHanssen 😉 https://nfcore.slack.com/archives/CELEMAGC9/p1657108775156149

matthdsm avatar Oct 13 '22 06:10 matthdsm

I can't see any aligner tests in the CI. Am I right?

matthdsm avatar Oct 13 '22 11:10 matthdsm

I can't see any aligner tests in the CI. Am I right?

https://github.com/nf-core/sarek/actions/runs/3240467988/jobs/5311130371

maxulysse avatar Oct 14 '22 06:10 maxulysse