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Add command nf-core subworkflows lint#2379

Merged
mirpedrol merged 16 commits into
nf-core:devfrom
mirpedrol:subworkflows-lint
Jul 26, 2023
Merged

Add command nf-core subworkflows lint#2379
mirpedrol merged 16 commits into
nf-core:devfrom
mirpedrol:subworkflows-lint

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@mirpedrol

@mirpedrol mirpedrol commented Jul 21, 2023 •
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Close #1887

Implement nf-core subworkflows lint command

  • implement command
  • add pytests
  • add lint tests
    • main.nf
    • meta.yml
    • changes compared to nf-core/modules repo
    • subworkflow tests
    • TODOs
    • version
  • Write documentation

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@codecov

codecov Bot commented Jul 21, 2023 •
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Codecov Report

Merging #2379 (c4071f6) into dev (5a6d2b0) will decrease coverage by 1.96%.
Report is 2 commits behind head on dev.
The diff coverage is 44.75%.

@@            Coverage Diff             @@
##              dev    #2379      +/-   ##
==========================================
- Coverage   73.09%   71.14%   -1.96%     
==========================================
  Files          79       87       +8     
  Lines        9026     9395     +369     
==========================================
+ Hits         6598     6684      +86     
- Misses       2428     2711     +283
Files Changed Coverage Δ
nf_core/components/components_utils.py 48.19% <ø> (ø)
nf_core/modules/lint/main_nf.py 68.28% <ø> (ø)
nf_core/modules/lint/meta_yml.py 60.00% <ø> (ø)
nf_core/subworkflows/lint/main_nf.py 9.70% <9.70%> (ø)
nf_core/subworkflows/lint/meta_yml.py 11.53% <11.53%> (ø)
nf_core/subworkflows/lint/subworkflow_tests.py 14.58% <14.58%> (ø)
nf_core/subworkflows/lint/__init__.py 28.37% <28.37%> (ø)
nf_core/subworkflows/lint/subworkflow_todos.py 28.57% <28.57%> (ø)
nf_core/subworkflows/lint/subworkflow_changes.py 30.00% <30.00%> (ø)
nf_core/subworkflows/lint/subworkflow_version.py 30.43% <30.43%> (ø)
... and 18 more

mirpedrol
mirpedrol commented Jul 25, 2023
View reviewed changes
Comment thread nf_core/modules/lint/__init__.py
Comment thread nf_core/subworkflows/lint/meta_yml.py
Comment thread nf_core/subworkflows/lint/subworkflow_tests.py Outdated
@mirpedrol mirpedrol marked this pull request as ready for review July 25, 2023 14:33
mashehu
mashehu approved these changes Jul 26, 2023
View reviewed changes
Comment thread README.md Outdated
Comment thread README.md Outdated
Comment thread README.md Outdated
Comment thread nf_core/__main__.py Outdated
Comment thread nf_core/__main__.py Outdated
Comment thread nf_core/components/lint/__init__.py Outdated
Comment thread nf_core/components/lint/__init__.py Outdated
Comment thread nf_core/components/nfcore_component.py Outdated
Comment thread nf_core/modules/lint/__init__.py
Comment thread nf_core/subworkflows/lint/meta_yml.py
@mirpedrol mirpedrol merged commit a520bfe into nf-core:dev Jul 26, 2023
@mirpedrol mirpedrol deleted the subworkflows-lint branch July 26, 2023 14:16
@mirpedrol mirpedrol mentioned this pull request Jul 26, 2023
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@mirpedrol @mashehu