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revert wfmash to v0.10.4 #192

Merged
merged 3 commits into from
Mar 25, 2024
Merged

revert wfmash to v0.10.4 #192

merged 3 commits into from
Mar 25, 2024

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subwaystation
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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 (nf-test test main.nf.test -profile test,docker).
  • 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).

We revert module wfmash to v0.10.4, because the current releases are unstable, not documented, and I don't understand how to set the parameters properly.

It is currently unclear, when a new stable release will become available. People like @baozg or @AndreaGuarracino are evaluating.

ewels
ewels reviewed Mar 25, 2024
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nextflow_schema.json Outdated Show resolved Hide resolved
subwaystation and others added 2 commits March 25, 2024 15:01
@subwaystation @ewels
Update nextflow_schema.json
d08c989 
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
@subwaystation
typo
e9ee042
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github-actions bot commented Mar 25, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e9ee042

+| ✅ 187 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • 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:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-25 14:04:27

@subwaystation subwaystation merged commit 5ece245 into dev Mar 25, 2024
15 checks passed
@subwaystation subwaystation deleted the wfmash_0104 branch March 25, 2024 14:12
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@subwaystation @ewels