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Module update + CI #52

Merged
merged 20 commits into from
Jan 24, 2024
Merged

Module update + CI #52

merged 20 commits into from
Jan 24, 2024

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kbestak
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@kbestak kbestak commented Jan 16, 2024 •
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#41

Updated mindagap, custom/dumpsoftwareversion and multiqc modules.
Updated the pipeline to handle new logic introduced in the new mindagap version including all parameters.
Updated base.config to handle ilastik's memory usage.

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!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • CHANGELOG.md is updated.

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github-actions bot commented Jan 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ae4c361

+| ✅ 162 tests passed       |+
!| ❗   5 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 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 main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-24 08:16:01

@kbestak
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kbestak commented Jan 16, 2024

Previous commit broke the CI

@kbestak kbestak changed the title Module update Module update + CI Jan 16, 2024
@kbestak kbestak requested a review from FloWuenne January 16, 2024 17:38
@kbestak kbestak self-assigned this Jan 16, 2024
@kbestak
metromap and logo update
181c2ac
@kbestak
Revert "metromap and logo update"
f37b992 
This reverts commit 181c2ac.

assets/nf-core-molkart_logo_light.png, docs/images/nf-core-molkart_logo_light.png, docs/images/nf-core-molkart_logo_dark.png should not be changed.
@kbestak
reverted previous commit and updated metromap
a81bb19
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kbestak commented Jan 19, 2024

@nf-core-bot fix linting please

nf-core-bot and others added 2 commits January 19, 2024 12:56
@nf-core-bot
[automated] Fix linting with Prettier
6d5f606
@FloWuenne
Update test_full.config
ae4c361 
Changed mindagap params for full test to reduce runtime.
FloWuenne
FloWuenne approved these changes Jan 24, 2024
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LGTM I think we are ready for a review! 🚀

@kbestak kbestak merged commit a729ac4 into nf-core:dev Jan 24, 2024
11 checks passed
@kbestak kbestak deleted the todo_module_update branch January 24, 2024 09:18
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@FloWuenne FloWuenne FloWuenne approved these changes

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