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Feature/extractumi #21
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…orkflows/modules into feature/extractumi
Fork Sync: Update from parent repository
…orkflows/modules into feature/extractumi
This reverts commit be48046.
Fork Sync: Update from parent repository
Fork Sync: Update from parent repository
Fork Sync: Update from parent repository
Fork Sync: Update from parent repository
Fork Sync: Update from parent repository
Fork Sync: Update from parent repository
Fork Sync: Update from parent repository
…kflows_develop Trigger github actions when PR is made against develop
On local, it looks like |
Yes I noticed this as well and haven't been able to get it to work locally. The pytest seems to work fine on git actions and the direct run of the nextflow test seems to work as well so not exactly sure what the issue is. I think it might be a bug coming from nf-core? I've only experienced this with subworkflows. @anoronh4 I think you observed this issue as well? |
try to remove all of |
stub test |
I used these commands to help with cleanup: |
This PR adds the
extractumi
workflow for access's uncollapsed bam generation.I've tested the workflow with:
nextflow run ./tests/subworkflows/nf-core/extractumi -entry test_extractumi -c ./tests/config/nextflow.config
, which was generatednf-core modules create-test-yml
.I've tried to keep this PR workflow specific, but being one of the first workflow PRs a few other small things are currently included:
extractumi
's test data is too big to fit ontools-test-dataset
instead I opted to include theinstall_data.sh
script, which can download our test data from google drive. The file is automatically sourced whennextflow run ./tests/subworkflows/nf-core/extractumi -entry test_extractumi -c ./tests/config/nextflow.config
is run.Let me know your thoughts! Open to any and all suggestions for how this can be restructured / what PR conventions we want to use moving forward.