fixing references to resources: 1kG for VQSR, dbsnp for Realignment s…

azzaea commented 7 years ago

…tage - Thank you Jennie Zermeno for pointing out

pvanheus commented 7 years ago

Can you please explain what this change does?

azzaea commented 7 years ago

Hello Peter, Yes, there were still some mistakes in the VQSR and Realignment steps:

It would require the 1000G file in the tools/GATK-VariantRecalibrator-SNPs.cwl , but it wasn't stated as dependency in the workflows/GATK/GATK-Sub-Workflow-h3abionet-snp.cwl. It also needed fixing in the json files provided for testing (/workflows/GATK/GATK-complete-WES-Workflow-h3abionet.dockstore.json, and /workflows/GATK/GATK-complete-WES-Workflow-h3abionet.json)
For the Mills, it used to refer to the 1000G file.
It used dbsnp for realignment, while the recommendation is not to use it for this stage: https://software.broadinstitute.org/gatk/documentation/article.php?id=1247

Thank you, Azza

pvanheus commented 7 years ago

Thanks. We really need to figure out how to test this.

h3abionet / h3agatk