Address MuTect requirement of uncompressed reference file

OpenGenomics / mc3

Apache License 2.0

34 stars 22 forks source link

Address MuTect requirement of uncompressed reference file #14

Closed kamichiotti closed 6 years ago

kamichiotti commented 6 years ago

Uncompressed reference FASTA is used to run mc3_variant.cwl while compressed FASTA are used in mc3_vcf2maf_full.cwl. Mutect appears to be the only one in need of an uncompressed reference file. Determine a workaround to eliminate the need of having both compressed and uncompressed versions in the reference directory.

kamichiotti commented 6 years ago

Placed prep_ref subworkflow into mc3_variant.cwl that unzips, indexes, and generates dict file. NOTE: In the future, this subworkflow will be moved to the workflow for generating the initial reference directory.