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Fix reported bugs #334

Merged
merged 3 commits into from Apr 3, 2024
Merged

Fix reported bugs #334

merged 3 commits into from Apr 3, 2024

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christopher-mohr
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@christopher-mohr christopher-mohr commented Apr 2, 2024 •
edited

Fixes

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).

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github-actions bot commented Apr 2, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f3df2e3

+| ✅ 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 2024-04-03 07:59:20

@ylang0825
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Great updating! I wonder how to apply this updated version? I use the parameter '-r dev' but found it still needs bowtie1.3.0-2. Thank you!

@christopher-mohr
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Great updating! I wonder how to apply this updated version? I use the parameter '-r dev' but found it still needs bowtie1.3.0-2. Thank you!

Hi @ylang0825, this still needs to be merged into the dev branch. But we need a review. I guess this will be done today.

@ylang0825
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@christopher-mohr Thanks!

apeltzer
apeltzer approved these changes Apr 3, 2024
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LGTM - changelog please?

@christopher-mohr christopher-mohr merged commit 151d33d into nf-core:dev Apr 3, 2024
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@christopher-mohr christopher-mohr deleted the fix_reported_bugs branch April 3, 2024 08:25
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@christopher-mohr @ylang0825 @apeltzer