Optimize OptitypePipeline.py input

[johnegarza]

docker-immuno_tools-cwl/optitype_script.sh

Line 55 in ef53b1e

python /usr/local/bin/OptiType/OptiTypePipeline.py -i $outdir/$name.hla.fwd.fastq $outdir/$name.hla.rev.fastq --dna -v -p $name -o $outdir

Currently, our script provides 2 fastq files to Optitype as input, which results in an unnecessary second alignment by Optitype itself as part of its internal pipeline. Providing mapped and filtered bams as input skips this step; this should also allow us to avoid a few other conversion steps in our prep script.

[johnegarza]

Update- providing our own bams as input may not work; if this is the case, it might not be possible to use a custom HLA reference (optitype has one built in) without modifying the optitype code itself, but I need to verify this