Update demux script - Githubissues

populationgenomics / saige-tenk10k

Hail batch pipeline to run SAIGE on CPG's GCP

MIT License

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Update demux script #164

Closed annacuomo closed 6 days ago

annacuomo commented 6 days ago

Update this script to take paths and common variant thresholds as inputs, move to helper.

For context, this is somewhat separate from the main pipeline, it is a script that generates a common SNP VCF file that gets transferred over to HPC so we can demultiplex (assign cells to their donor of origin in a pool experiment, using vireo) our scRNA-seq data.

This happens upstream of the pipeline, so it goes:

scRNA-seq processing up to demultiplexing (over at HPC)
in parallel, WGS processing (large cohort pipeline)
this script
scRNA-seq can resume processing, starting with demultiplexing, up to making the input files required for the SAIGE-QTL pipeline
SAIGE-QTL pipeline can run (this repo)

Long slack thread for when this was first run for additional context: https://centrepopgen.slack.com/archives/C018KFBCR1C/p1703025906749599

annacuomo commented 6 days ago

Given that this is a rename and a change the GitHub diff is... not useful. Happy to rubber stamp this

I know right?! Should I have done something different? I don't know what rubber stamp means but I say do it (unless it just means approve which you already did?)!