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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.com/
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NF Optitype #224

Closed evanbiederstedt closed 5 years ago

evanbiederstedt commented 5 years ago

https://hub.docker.com/r/fred2/optitype

So, Chai reminded me that HLA Polysolver might take forever to run, and it's old. Poorly-written perl scripts.

We discuss this, but let's use Optitype as well: https://hub.docker.com/r/fred2/optitype/dockerfile https://hub.docker.com/r/zlskidmore/optitype

I would use this as the main part of the pipeline; for now, out the HLA Polysolver files, but use Optitype instead

The nice thing about the Docker images above is that they include the MIP solvers

kpjonsson commented 5 years ago

FWIW: In previous discussions we scrapped the idea of Optitype because it takes as input FASTQ files.

evanbiederstedt commented 5 years ago

FWIW: In previous discussions we scrapped the idea of Optitype because it takes as input FASTQ files.

We could try do bam2fastq I suppose.

Though....if the pipeline is connected, we could put Optitype in the BAM alignment step, or wherever. I think that's a better idea actually....

allanbolipata commented 5 years ago

Removing myself as assignee since it seems like this one is on the backburner

kpjonsson commented 5 years ago

Not sure this is still relevant, close?

evanbiederstedt commented 5 years ago

For our purposes, we can close I think