Fastqc checking

[azzaea]

This change corrects the path of fastqc.cwl when called to run from fastqc_workflow.cwl; and also renames the output folder name to fastqc.

[pvanheus]

Thanks @zo0z - can you please comment on your VQSR related changes? What was wrong that is now fixed?

[azzaea]

Yes,

• For snps, the omni database is well curated, so it should be specified as: truth=true, also, the `1000G is recommended to be a resource. I also changed the prior probablity for dbsnp to 2 (as per the recommendations here)
• For indels, only Mills and dbsnp should be used as resources for the recalibration, and also the annotations specified in the file were for snps. A slightly different annotations were recommended by the GATK forum.

The cwlviewer has been really handy in picking up these