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Merged
merged 9 commits into from
May 2, 2024
Merged

Empty ref to samtools sort #60

merged 9 commits into from
May 2, 2024

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JackCurragh
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This PR corrects issue #59. An empty value is now passed to SAMTOOLS_SORT

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/riboseq 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 May 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4af68a2

+| ✅ 175 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: assets/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-02 12:22:23

maxulysse
maxulysse reviewed May 2, 2024
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CHANGELOG.md
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what happened to CHANGELOG?

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That is a great question. Looks like I thought I worked out prettier but instead it just deleted everything in the file...

FelixKrueger
FelixKrueger approved these changes May 2, 2024
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Looks good.

@JackCurragh JackCurragh merged commit d110805 into dev May 2, 2024
@JackCurragh JackCurragh deleted the empty_ref_to_samtools_sort branch May 3, 2024 07:39
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@maxulysse maxulysse maxulysse left review comments

@FelixKrueger FelixKrueger FelixKrueger approved these changes

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@JackCurragh @maxulysse @FelixKrueger @pinin4fjords