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Merged
maxulysse merged 8 commits into from
Mar 24, 2025
Merged

add GPUS testing possibility #1835

maxulysse merged 8 commits into from
Mar 24, 2025

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@maxulysse
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@maxulysse maxulysse commented Mar 13, 2025

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
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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nf-core-bot commented Mar 13, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

maxulysse
maxulysse commented Mar 13, 2025
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maxulysse
maxulysse commented Mar 13, 2025
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maxulysse
maxulysse commented Mar 13, 2025
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@maxulysse maxulysse mentioned this pull request Mar 13, 2025
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famosab commented Mar 14, 2025

I think this looks good but I am not an expert on anything related to GHA haha

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famosab commented Mar 14, 2025

Do we also need to extend the nf-test.config to include gpu settings (similar to modules repo) or does nextflow do this automatically?

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famosab commented Mar 14, 2025

Something like this in the nextflow config

gpu {
        process {
            withLabel: process_gpu {
                ext.use_gpu = true
            }
        }
        docker.runOptions = '-u $(id -u):$(id -g) --gpus all'
        apptainer.runOptions = '--nv'
        singularity.runOptions = '--nv'
    }

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famosab commented Mar 14, 2025

or a test profile for gpus

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maxulysse commented Mar 14, 2025

Possibly, I think that can be included in the parabricks PR.
I did just have a go at the GHA

FriederikeHanssen
FriederikeHanssen reviewed Mar 14, 2025
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tests/start_from_markduplicates.nf.test.snap
Comment on lines -614 to -615
"test.md.cram.stats:md5,f181d98f08ad94c3926ac149a87d834b",
"test.recal.cram.stats:md5,18346c938c7b1bfaf9ac9413fdba90d8"
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@FriederikeHanssen FriederikeHanssen Mar 14, 2025

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what happened to the checksums?

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@maxulysse maxulysse Mar 14, 2025

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Famke removed some cram.stats, because they were unstable, so I removed them all

FriederikeHanssen
FriederikeHanssen reviewed Mar 14, 2025
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FriederikeHanssen
FriederikeHanssen reviewed Mar 14, 2025
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@FriederikeHanssen FriederikeHanssen mentioned this pull request Mar 24, 2025
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@maxulysse maxulysse merged commit e8009c4 into nf-core:dev Mar 24, 2025
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@maxulysse maxulysse deleted the GPUS branch April 25, 2025 08:05
@maxulysse maxulysse restored the GPUS branch April 25, 2025 08:05
@edmundmiller edmundmiller linked an issue May 12, 2025 that may be closed by this pull request
Sarek goes GPU - parabricks integration #1853
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Sarek goes GPU - parabricks integration

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@maxulysse @nf-core-bot @famosab @FriederikeHanssen