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Add warning GTDB-TK results will be empty if no contigs pass completeness filter #565

Merged
merged 6 commits into from
Feb 1, 2024
Merged

Add warning GTDB-TK results will be empty if no contigs pass completeness filter #565

merged 6 commits into from
Feb 1, 2024

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jfy133
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@jfy133 jfy133 commented Feb 1, 2024

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>).
  • 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 Feb 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c49febd

+| ✅ 211 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ 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 WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-01 20:36:59

CarsonJM
CarsonJM reviewed Feb 1, 2024
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jfy133
jfy133 commented Feb 1, 2024
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jfy133 commented Feb 1, 2024

@nf-core-bot fix linting

@jfy133 jfy133 merged commit 601114d into dev Feb 1, 2024
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@jfy133 jfy133 deleted the warn-when-gtdb-filter-empty branch February 1, 2024 20:57
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@CarsonJM CarsonJM CarsonJM approved these changes

@HadrienG HadrienG Awaiting requested review from HadrienG

@maxibor maxibor Awaiting requested review from maxibor

@prototaxites prototaxites Awaiting requested review from prototaxites

@gregorysprenger gregorysprenger Awaiting requested review from gregorysprenger

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@jfy133 @CarsonJM @nf-core-bot