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Fix auto-detection of adapter with fastp #337

Merged
merged 2 commits into from
Apr 5, 2024
Merged

Fix auto-detection of adapter with fastp #337

merged 2 commits into from
Apr 5, 2024

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christopher-mohr
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Fixes #326.

With this change it is possible to enable fastp adapter auto-detection using the parameter value "auto-detect".

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 (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

@christopher-mohr christopher-mohr changed the title accept auto-detect as parameter value to activate Fix auto-detection of adapter with fastp Apr 4, 2024
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github-actions bot commented Apr 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2bfbbd5

+| ✅ 181 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 2.13.1
  • Run at 2024-04-04 08:23:58

jfy133
jfy133 approved these changes Apr 5, 2024
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One comment about possible missing update, but otherwise LGTM

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@christopher-mohr
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One comment about possible missing update, but otherwise LGTM

Thank you!

@christopher-mohr christopher-mohr merged commit 38b898a into nf-core:dev Apr 5, 2024
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@christopher-mohr christopher-mohr deleted the fix_adapter_param branch April 5, 2024 09:02
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@jfy133 jfy133 jfy133 approved these changes

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