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Removed untar, updated bowtie_channel #452

Merged
merged 3 commits into from
Oct 1, 2024
Merged

Removed untar, updated bowtie_channel #452

merged 3 commits into from
Oct 1, 2024

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nschcolnicov
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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/smrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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 Sep 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b79dccb

+| ✅ 230 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-10-01 11:49:14

@nschcolnicov nschcolnicov marked this pull request as ready for review October 1, 2024 11:47
atrigila
atrigila approved these changes Oct 1, 2024
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@atrigila atrigila left a comment

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Perfect! Great job

subworkflows/local/prepare_genome/main.nf
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We should move the CLEAN_FASTA after the if(val_fasta)

if(val_fasta) {
        // Clean fasta (replace non-ATCGs with Ns, remove whitespaces from headers)
        CLEAN_FASTA ( ch_fasta )
        ch_versions      = ch_versions.mix(CLEAN_FASTA.out.versions)
        
        // Set channels: clean fasta and its index
        ch_fasta         = CLEAN_FASTA.out.output

@nschcolnicov nschcolnicov merged commit 2016dac into nf-core:dev Oct 1, 2024
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@nschcolnicov nschcolnicov mentioned this pull request Oct 1, 2024
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@atrigila atrigila atrigila approved these changes

@apeltzer apeltzer Awaiting requested review from apeltzer

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@nschcolnicov @atrigila