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Add documentation how to produce multiple Bracken2 taxonomic level reports #605

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Merged
merged 1 commit into from
Apr 29, 2025
Merged

Add documentation how to produce multiple Bracken2 taxonomic level reports #605

merged 1 commit into from
Apr 29, 2025

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jfy133
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@jfy133 jfy133 commented Apr 29, 2025 •
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Closes #410

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 pipelines 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).

@jfy133 jfy133 linked an issue Apr 29, 2025 that may be closed by this pull request
Allow multiple bracken profiles with different -l levels from the same kraken2 report #410
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sofstam
sofstam approved these changes Apr 29, 2025
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github-actions bot commented Apr 29, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8cceca3

+| ✅ 279 tests passed       |+
!| ❗  17 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • local_component_structure - krona_cleanup.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - kraken2_standard_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_complexityfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - visualization_krona.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - nonpareil.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - standardisation_profiles.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_filtering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-04-29 07:49:55

@jfy133 jfy133 merged commit a79a034 into dev Apr 29, 2025
14 of 26 checks passed
@jfy133 jfy133 deleted the bracken2-levels branch April 29, 2025 10:55
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Allow multiple bracken profiles with different -l levels from the same kraken2 report
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@jfy133 @sofstam