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UCSF-DSCOLAB / data_processing_pipelines

A repository to store the existing pipelines to process the various CoLabs datasets
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working commit of the fmx-assign-to-gt functionality #44

Open erflynn opened 10 months ago

erflynn commented 10 months ago

Addresses #23

Adds optional function to run gtcheck to compare reference vcf and freemuxlet output.

erflynn commented 10 months ago

@amadeovezz -- can you check that these additions to the pre_qc file follow conventions you have set up for channels? would love feedback on this.

amadeovezz commented 9 months ago

@erflynn granted my hotfix testing PR works (and the subsequently merged in). Do you want to try and adding a test cases for this? Seems like a good candidate.

amadeovezz commented 9 months ago

@amadeovezz -- can you check that these additions to the pre_qc file follow conventions you have set up for channels? would love feedback on this.

ya i was actually looking at the channel logic, i think we can refactor it to make it simpler.