Add tx2gene module (formerly local to rnaseq)#4854
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pinin4fjords merged 10 commits intomasterfrom Feb 6, 2024
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Want me to wait for nf-core/test-datasets#1083 before reviewing? |
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No, go right ahead. I'll update the test data reference, but everything else should be good |
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I don't like how the error is handled, but since this is a port I think we should go with it and add an additional test in future.
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
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* Add test data link * Add tx2gene * Fix linting, update snapshots * path -> directory * Correct conda setup * Correct conda setup * Update test data reference * Apply minor suggestions from code review Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Error out at point of failure in determining transcript attribute --------- Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
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* Add test data link * Add tx2gene * Fix linting, update snapshots * path -> directory * Correct conda setup * Correct conda setup * Update test data reference * Apply minor suggestions from code review Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Error out at point of failure in determining transcript attribute --------- Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
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* Add test data link * Add tx2gene * Fix linting, update snapshots * path -> directory * Correct conda setup * Correct conda setup * Update test data reference * Apply minor suggestions from code review Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Error out at point of failure in determining transcript attribute --------- Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
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nf-core/test-datasets#1083 should be merged first, and appropriate adjustments made here.
PR checklist
versions.ymlfile.labelPROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware