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Add flag to publish intermediate bracken files #491

Merged
merged 10 commits into from
May 31, 2024
Merged

Add flag to publish intermediate bracken files #491

merged 10 commits into from
May 31, 2024

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sofstam
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@sofstam sofstam commented May 23, 2024

Fixes the bug reported here

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/taxprofiler 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 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ee31ff0

+| ✅ 258 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-30 09:01:23

jfy133
jfy133 reviewed May 24, 2024
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sofstam commented May 24, 2024

Realised that yesterday looking at the docs of publishDir. Still not working, I found another example and maybe we can provide the condition in the path.

@sofstam sofstam marked this pull request as ready for review May 30, 2024 08:35
@sofstam sofstam requested a review from jfy133 May 30, 2024 08:35
jfy133
jfy133 reviewed May 30, 2024
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Need a changelog update (you can can add Emily Wissel as the reporter)

docs/output.md Outdated Show resolved Hide resolved
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sofstam and others added 4 commits May 30, 2024 10:45
@sofstam
Update CHANGELOG.md
e148948
@sofstam @jfy133
Update nextflow_schema.json
892782f 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@sofstam @jfy133
Update docs/output.md
fffe8e1 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@sofstam
Update output.md
ca29906
jfy133
jfy133 reviewed May 30, 2024
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@jfy133 jfy133 merged commit a6475c5 into nf-core:dev May 31, 2024
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@sofstam @jfy133