Arvados

branch 17049-make-singlechrom, commit d2f6d47da38e96de4597bb58ba1193e261af8fb1

I finished a run for chr19 input fastqs for 5 samples.
https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-3dqeqodgi1usk0r

I encountered a gatk bug that the memory usage spikes when writing result vcf in the haplotypecaller step, if the region is outside of chr19. (And in general, in regions when very few reads are placed.) I had to schedule 14G ram machines for that step to complete it. (See failure https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-v0sq9csiz1p94nx)

Also I had to upload a different docker image for curii/clinvar-report to keep in order to finish the gvcf-to-vcf step (see failure https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-zulp4y3e9f7tv59). The new docker image is https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-kl40n4746vmjnw2

Input fastqs here https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-j1jotbx4uqckkec
The run for generating the chr19 input fastqs is https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-ilo79fgj728afkl

commit d147d1d1fafeeea06bd09d9479337b0f5aab43b0

Added comments for the singe chrom chr19 yml.