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@buehlere buehlere commented May 18, 2023

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 generated nf-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 on tools-test-dataset instead I opted to include the install_data.sh script, which can download our test data from google drive. The file is automatically sourced when nextflow run ./tests/subworkflows/nf-core/extractumi -entry test_extractumi -c ./tests/config/nextflow.config is run.
  • adding some gitignores

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.

buehlere and others added 16 commits May 30, 2023 20:47
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
@huyu335
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huyu335 commented Jun 27, 2023

On local, it looks like nf-core subworkflows test extractumi and pytest --tag subworkflows/extractumi --symlink --kwdof --git-aware --color=yes were not working for me. They took 2 hours and failed without clear error(probably out of memory or timeout). But nextflow run ./tests/subworkflows/nf-core/extractumi -entry test_extractumi -c ./tests/config/nextflow.config worked.

@buehlere
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buehlere commented Jun 27, 2023

On local, it looks like nf-core subworkflows test extractumi and pytest --tag subworkflows/extractumi --symlink --kwdof --git-aware --color=yes were not working for me. They took 2 hours and failed without clear error(probably out of memory or timeout). But nextflow run ./tests/subworkflows/nf-core/extractumi -entry test_extractumi -c ./tests/config/nextflow.config worked.

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?

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buehlere commented Jul 7, 2023

try to remove all of install_data.sh function.

@buehlere
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buehlere commented Jul 21, 2023

stub test

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buehlere commented Aug 8, 2023

I used these commands to help with cleanup:
git checkout develop modules/nf-core/bcftools/
git checkout develop modules/nf-core/tabix/
git checkout develop subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/
git checkout develop tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/
git checkout develop tests/modules/nf-core/tabix/
git checkout develop tests/modules/nf-core/bcftools/
git checkout develop tests/config/pytest_modules.yml
git rm .github/workflows/sync-action.yml
and then did a full merge with develop

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3 participants