Parabricks starfusion #9150
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Parabricks starfusion #9150
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Updating branch with most recent updates from Master
famosab
reviewed
Sep 29, 2025
famosab
reviewed
Sep 29, 2025
…orkflows/nf-core-modules into parabricks_starfusion
famosab
reviewed
Sep 30, 2025
….out.junction from rnafq2bam)
famosab
reviewed
Oct 14, 2025
.github/workflows/nf-test-gpu.yml
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| nf-test-gpu: | ||
| runs-on: "runs-on=${{ github.run_id }}/family=g4dn.xlarge/image=ubuntu24-gpu-x64" | ||
| runs-on: "runs-on=${{ github.run_id }}/family=g4dn.8xlarge/image=ubuntu24-gpu-x64" |
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looks good to me its just this change where I am unsure
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Based on the other PR it looks like it's okay for me to change it back before merging. And we'll have some discussions elsewhere about if there's a better way we can do this in the future.
… match g4dn.2xlarge
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famosab
approved these changes
Oct 15, 2025
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vagkaratzas
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Oct 24, 2025
* Creating new module folder for starfusion, using fq2bam as a starting point * resolving commit issue * Updating files to reflect starfusion instead of fq2bam. Tests not passing. * Parabricks is running but failing. Must be an issue with the input data. * Creating new starfusion_build folder. Copied from starfusion. * Changing to using starfusion/build as base for new parabricks starfusion model * Decremented starfusion_build to 1.7 for Parabricks compatibility * Tested and linted new starfusion model * Removing GPU docker options from nextflow.config * Adding support for Chimeric.out.junction output in rnafq2bam * Updating language in README.md * Adding version checking to snapshot assertion * Adding out_dir to test assertions * Removing stub fail test * Cleaning up data outputs * Removing unnecessary tags from starfusion nftest * Cleaning up tags in starfusion_build nftest * Added test for chimeric output in rnafq2bam * Fixing issue with empty output (problem was with passing the chimeric.out.junction from rnafq2bam) * Changing to starfusion test dataset to fix empty junction file * Making Chimeric.out.junction output detection more generic * Cleaning up rnafq2bam test assertions * Changing starfusion to output fusions and abridged fusions (for parity with baseline starfusion module) and cleaning up test assertions * Removing chimeric tests due to hanging issue with CI runners * Reducing memory requirements * Updating mem requiremnts * ci: Try 12xl * Brining back chimeric tests * Increasing CI runner GPU size * Updating chimeric.out.junction snapshot in rnafq2bam * Upgrading memory from 15 GB to 100 GB to meet minimum recommended requirements * Chimeric.out.junction snapshot is not stable, so moving to just check file name and not contents * Moving module params out of the config and into the test file * Updating test data paths * Updating readme * Adding version printing back to snapshot * Adding version printing back to snapshot (more places) * Cleaning up module args * Removing compatible versions from module (since it does not work) * Scaling down instance size to match minimum system requirements * Updating stub test * Updating module outputs * Updating stub test * Updating meta.yml to match new module outputs * Adding rnafq2bam snapshot * Updating rnafq2bam outputs to fix stub test * Fixing starfusion stub tests * Updating README to include notes on testing for starfusion module * Updating README to reflect new large instance for testing starfusion * Updating to 4.6 * Adjusting memory requirements for rnafq2bam and starfusion testing to match g4dn.2xlarge * Reverting github ci runner instance --------- Co-authored-by: Edmund Miller <[email protected]>
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PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda