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Template update #93

Merged
merged 19 commits into from
Oct 25, 2024
Merged

Template update #93

merged 19 commits into from
Oct 25, 2024

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fasterius
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PR for checking that template updates work as expected.

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github-actions bot commented Oct 23, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit af8d1b0

+| ✅ 190 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: assets/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-25 13:36:07

@fasterius fasterius force-pushed the template-update branch 3 times, most recently from e938c8b to 1ae6576 Compare October 24, 2024 12:49
@fasterius
Do not validate input in pipeline initialisation
2321e61
@fasterius
Fix missing dollar sign in GHA
ccf0084
@fasterius
Fix GHA job names
d9ec30f
@fasterius
Remove remaining usage of old check_max()
5b7b81a
@fasterius
Fix missing test profile from nf-test default
09b6fc7
@fasterius
Add patch for spaceranger/count
29a3db7
@fasterius
Pin scipy version in Conda environment
f3a218e
@fasterius
Fix test profile resource limits
99f2fb5 
The `spaceranger/count` module stalled during GHA CI tests due to some
issue with the new template resource specifications for the test
profile. The new template specifies 15 GB of RAM, but the GHA runner
only had 13.6 available, which somehow lead to a stall of the task until
the time ran out. Setting a slightly lower memory requirement fixes
this.
@fasterius fasterius merged commit aa3472a into dev Oct 25, 2024
2 checks passed
@fasterius fasterius deleted the template-update branch October 25, 2024 13:38
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@fasterius @nf-core-bot