recalibrate: gatk running on a single CPU thread for multiple samples

[Ivan De Dios]

Hi Brad,

I noticed gatk base-recalibrator starting up on only a single thread for a run with 96 bam files. This is from a previously failed run where variant calling finished for vardict and platypus but mutect2 failed due to "malformed header" errors in the bam files. So I adjust the yaml config to include realignment and recalibration for gatk.

I ran it as bcbio_nextgen.py ../config/run.yaml -n 28

[Brad Chapman]

Ivan;
If you're re-running in the same directory and want to re-parallelize steps
you need to remove `checkpoints_parallel/*.done` files to tell bcbio that
you're re-running these steps:

http://bcbio-nextgen.readthedocs.io/en/latest/contents/parallel.html#troubleshooting

Hope that gets the analysis running in parallel as expected,
Brad


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