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check_up_to_date() also checks for subworkflows#1934

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mirpedrol merged 8 commits into
nf-core:devfrom
mirpedrol:checkuptodate
Oct 12, 2022
Merged

check_up_to_date() also checks for subworkflows#1934
mirpedrol merged 8 commits into
nf-core:devfrom
mirpedrol:checkuptodate

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@mirpedrol

@mirpedrol mirpedrol commented Oct 11, 2022

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The check_up_to_date() function from modules_json.py also checks for subworkflows.
This also fixes the issue when installing a subworkflow from a new modules repo. To test:

nf-core create # Create a new test pipeline
nf-core subworkflows --git-remote https://gitlab.com/nf-core/modules-test.git --branch subworkflows install bam_sort_samtools # try installing a subworkflow from a new remote

close #1917

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

Comment thread nf_core/modules/modules_json.py Outdated
Comment thread nf_core/modules/modules_json.py Outdated
Comment thread nf_core/modules/modules_json.py Outdated
Comment thread nf_core/modules/modules_json.py Outdated
Comment thread nf_core/subworkflows/install.py Outdated
mirpedrol and others added 3 commits October 12, 2022 10:29
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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codecov Bot commented Oct 12, 2022

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Codecov Report

Merging #1934 (a4b4645) into dev (865cae8) will increase coverage by 0.00%.
The diff coverage is 0.00%.

@@           Coverage Diff           @@
##              dev    #1934   +/-   ##
=======================================
  Coverage   60.03%   60.04%           
=======================================
  Files          37       37           
  Lines        4642     4640    -2     
=======================================
- Hits         2787     2786    -1     
+ Misses       1855     1854    -1     
Impacted Files Coverage Δ
nf_core/subworkflows/install.py 14.50% <0.00%> (+0.21%) ⬆️
nf_core/modules/test_yml_builder.py 49.09% <0.00%> (-0.46%) ⬇️

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@mirpedrol mirpedrol merged commit 5be0720 into nf-core:dev Oct 12, 2022
@mirpedrol mirpedrol deleted the checkuptodate branch October 12, 2022 08:58
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2 participants