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Remove defaults channel from remaining modules #58

Merged
merged 8 commits into from
Mar 14, 2025
Merged

Remove defaults channel from remaining modules #58

merged 8 commits into from
Mar 14, 2025

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prototaxites
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Fixes:

  • mitohifi - update to newest version of module
  • hifiasm - patch environment file to remove channel
  • oatk - update to newest version of module
  • minimap2/index - patch environment file to remove channel
  • lib/Utils.groovy channel check

I patched the modules for hifiasm and minimap2/align as the newer module versions come with software version updates.

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

ksenia-krasheninnikova
ksenia-krasheninnikova approved these changes Feb 7, 2025
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@ksenia-krasheninnikova ksenia-krasheninnikova left a comment

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Looks good to me. The local test generates all expected files. Linting is supposed to be fixed after template update.

@muffato
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muffato commented Feb 11, 2025

This is very good, thank you ! For the record, we're still working with Marcela on fixing the MitoHifi container. Once it's done, I'll let you know.
Apart from that, all containers in this PR are safe to use 👍🏼

@prototaxites
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@muffato Quick prod about the best option here for the GitHub actions - force merge and fix elsewhere, or just change them in this PR?

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github-actions bot commented Mar 11, 2025 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3b758cf

+| ✅ 130 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomeassembly_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomeassembly_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomeassembly_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-genomeassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomeassembly/genomeassembly/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2025-03-12 18:37:20

@muffato muffato merged commit d0b909c into dev Mar 14, 2025
4 of 6 checks passed
@muffato muffato deleted the conda-fix branch March 14, 2025 10:40
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muffato commented Mar 14, 2025

@muffato Quick prod about the best option here for the GitHub actions - force merge and fix elsewhere, or just change them in this PR?

Hi @prototaxites . I've merged the PR as it is. I'll let you fix the CI separately (especially since I see other PRs being worked on at the same time)

This was referenced Apr 10, 2025
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@muffato muffato muffato approved these changes

@ksenia-krasheninnikova ksenia-krasheninnikova ksenia-krasheninnikova approved these changes

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@prototaxites @muffato @ksenia-krasheninnikova