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Switch CI to nf-core/setup-nextflow action #1650

Merged
merged 9 commits into from
Jun 22, 2022
Merged

Switch CI to nf-core/setup-nextflow action #1650

merged 9 commits into from
Jun 22, 2022

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MillironX
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@MillironX MillironX commented Jun 21, 2022

Switches the workflows in this repo and the template to point to use setup-nextflow, rather than try to manually install Nextflow in a run: block. This allows for simplifying the execution matrix, and removes the need to keep track of whether a stable or edge release is actually the most recent.

PR checklist

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

@MillironX MillironX requested a review from ewels June 21, 2022 19:52
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@ewels ewels left a comment

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Nice!

Can maybe also remove the CAPSULE_LOG: none env vars too (see nf-core/setup-nextflow#1 )

Also update if we're moving to nf-core, as discussed in Slack 👍🏻

Otherwise LGTM! 💥

@MillironX
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Converting to draft until two things are fixed:

  1. Linting checks need to target the new matrix format
  2. Action should point to https://github.com/nf-core/setup-nextflow

@MillironX MillironX marked this pull request as draft June 21, 2022 20:04
@ewels ewels added the WIP Work in progress label Jun 21, 2022
@MillironX MillironX marked this pull request as ready for review June 21, 2022 20:38
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Tests are now passing, so this is actually ready for review.

@MillironX MillironX removed the WIP Work in progress label Jun 21, 2022
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codecov bot commented Jun 21, 2022

Codecov Report

Merging #1650 (0bab55b) into dev (7f8fa83) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##              dev    #1650   +/-   ##
=======================================
  Coverage   64.84%   64.84%           
=======================================
  Files          54       54           
  Lines        6270     6270           
=======================================
  Hits         4066     4066           
  Misses       2204     2204           
Impacted Files Coverage Δ
nf_core/bump_version.py 89.83% <ø> (ø)
nf_core/lint/actions_ci.py 89.09% <100.00%> (ø)

Continue to review full report at Codecov.

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@ewels ewels left a comment

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Just a few lurking CAPSULE_LOG env vars left I think? Otherwise the code LGTM 👍🏻

tests/test_bump_version.py Show resolved Hide resolved
@MillironX MillironX changed the title Switch CI to MillironX/setup-nextflow action Switch CI to nf-core/setup-nextflow action Jun 22, 2022
@ewels ewels merged commit 5f97960 into nf-core:dev Jun 22, 2022
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2 participants