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Replace local blat for nf-core blat in contaminant filter subworkflow #397

Merged
merged 26 commits into from
Sep 4, 2024
Merged

Replace local blat for nf-core blat in contaminant filter subworkflow #397

merged 26 commits into from
Sep 4, 2024

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atrigila
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@atrigila atrigila commented Aug 29, 2024 •
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Fixes #354
Closes #395

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).
  • 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).

@atrigila atrigila self-assigned this Aug 29, 2024
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github-actions bot commented Aug 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 496779c

+| ✅ 217 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 2024-09-04 19:32:05

@atrigila atrigila marked this pull request as ready for review August 29, 2024 21:29
@nschcolnicov
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I saw one particular issue in the pipeline, where a module wasn't running on all samples, the issue has been in the pipeline since the latest master release, more info here: #398.

I will take this opportunity to rebuild the nf-tests, using the info from #393 to subset considerably the files that we are testing for, since we are having to rewrite the tests too many times due to intermediate files changing.

@atrigila
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I agree. I have made several significant improvements and found some bugs while correcting the code. I think we first focus on determining which files are relevant.

@nschcolnicov
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I will update the tests to include the changes in the non-deterministic files, then please pull the changes and re run the tests. Thanks!

nschcolnicov
nschcolnicov approved these changes Sep 4, 2024
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LGTM!

@apeltzer apeltzer merged commit 874ef64 into nf-core:dev Sep 4, 2024
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@atrigila atrigila mentioned this pull request Sep 4, 2024
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@atrigila @nschcolnicov @apeltzer