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Add TAXPASTA_STANDARDISE support #303

Merged
merged 4 commits into from
Jun 11, 2023
Merged

Add TAXPASTA_STANDARDISE support #303

merged 4 commits into from
Jun 11, 2023

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jfy133
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@jfy133 jfy133 commented Jun 4, 2023

So taxpasta merge doesn't fail when only a single sample is passed through the pipeline.

resolves #282

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 (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).

@jfy133 jfy133 linked an issue Jun 4, 2023 that may be closed by this pull request
TAXPASTA_MERGE failing if only one sample provided. Add warning or single sample handling. #282
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github-actions bot commented Jun 4, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 321a2b8

+| ✅ 158 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_lint - Schema 'description' should be 'Taxonomic classification and profiling of shotgun and long-read metagenomic data'
    Found: 'Taxonomic classification and profiling of shotgun metagenomic data'

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-10 10:05:45

@jfy133 jfy133 requested a review from a team June 4, 2023 17:17
Midnighter
Midnighter approved these changes Jun 10, 2023
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Super solid work, thanks 😃

subworkflows/local/standardisation_profiles.nf Outdated Show resolved Hide resolved
@jfy133 jfy133 merged commit 2f1f0a8 into dev Jun 11, 2023
@jfy133 jfy133 deleted the taxpasta-single-sample branch June 11, 2023 15:10
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TAXPASTA_MERGE failing if only one sample provided. Add warning or single sample handling.
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@jfy133 @Midnighter