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Fix GTDB-Tk directory input#646

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jfy133 merged 3 commits intonf-core:devfrom
prototaxites:fix_gtdb_dir_input
Aug 3, 2024
Merged

Fix GTDB-Tk directory input#646
jfy133 merged 3 commits intonf-core:devfrom
prototaxites:fix_gtdb_dir_input

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@prototaxites prototaxites commented Aug 2, 2024 •
edited by tnmquann
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Change processing of GTDB directory input parameter so it's processed as a value rather than a queue channel.

Fixes #641

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/mag 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 Aug 2, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5b9c4f1

+| ✅ 307 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-02 08:25:43

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jfy133 commented Aug 3, 2024

First round of thanks Jim !

@jfy133 jfy133 merged commit a4adc3d into nf-core:dev Aug 3, 2024
@prototaxites prototaxites deleted the fix_gtdb_dir_input branch August 7, 2024 10:36
@jfy133 jfy133 mentioned this pull request Aug 22, 2024
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