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Migrate to nf-core bowtie align in contaminant filter #441

Merged
merged 19 commits into from
Sep 26, 2024
Merged

Migrate to nf-core bowtie align in contaminant filter #441

merged 19 commits into from
Sep 26, 2024

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atrigila
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@atrigila atrigila commented Sep 25, 2024 •
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#436

The scope of this PR is to migrate all instances of local bowtie to nf-core bowtie. The code in contaminant filter can still be heavily refactored but this is part of #406 .

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 25, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1438a91

+| ✅ 231 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 2024-09-25 18:26:53

@atrigila atrigila marked this pull request as ready for review September 25, 2024 19:18
nschcolnicov
nschcolnicov approved these changes Sep 25, 2024
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LGTM

@nschcolnicov nschcolnicov mentioned this pull request Sep 25, 2024
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@apeltzer apeltzer merged commit 586ef69 into nf-core:dev Sep 26, 2024
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@nschcolnicov nschcolnicov nschcolnicov approved these changes

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@atrigila @nschcolnicov @apeltzer