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Add config mode to nf-core mirtrace/qc #420

Merged
merged 8 commits into from
Sep 11, 2024
Merged

Add config mode to nf-core mirtrace/qc #420

merged 8 commits into from
Sep 11, 2024

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atrigila
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@atrigila atrigila commented Sep 11, 2024 •
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Fixes #419

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 11, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5d39fc9

+| ✅ 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 2024-09-11 15:22:57

@atrigila atrigila marked this pull request as draft September 11, 2024 13:52
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Some tests are failing (and will be updated) because the new module changed the way of naming the samples in the mirtrace files. Originally, it used the name of the file e.g. https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/trimmed/small_Clone1_N1.fastp.fastq.gz while it now uses the sample id from the samplesheet which is more appropriate.

original naming:
image

current naming:
image

@atrigila atrigila marked this pull request as ready for review September 11, 2024 15:44
apeltzer
apeltzer approved these changes Sep 11, 2024
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Very nice solution 👍🏻

@apeltzer apeltzer merged commit 8fa1018 into nf-core:dev Sep 11, 2024
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@apeltzer apeltzer apeltzer approved these changes

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