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Add metric parameter suffixes #155

Merged
merged 6 commits into from
Oct 17, 2023
Merged

Add metric parameter suffixes #155

merged 6 commits into from
Oct 17, 2023

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heringerp
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@heringerp heringerp commented Oct 17, 2023

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/pangenome 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).

Add parsing for metric parameter suffixes (and corresponding test) for the parameters

  • wfmash_sequence_length
  • wfmash_block_length
  • seqwish_transclose_batch

according to #120

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github-actions bot commented Oct 17, 2023

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 49dce5b

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in WorkflowPangenome.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-17 15:03:03

@subwaystation subwaystation self-requested a review October 17, 2023 13:13
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@subwaystation subwaystation left a comment

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See my comments.

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LGTM!

@heringerp heringerp merged commit 8362eee into nf-core:dev Oct 17, 2023
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2 participants