There is already a CWL and operator for IGV Reports, need to integrate it into the workflow somewhere.
It requires bam files and variant input files, so that will be a consideration
Also, it needs a list of regions to use for snapshotting, currently the CWL expects a .vcf sites file. But that is kind of awkward to generate, need to enable options for .bed and/or maf files.
The variant files also currently have to be .vcf, there is a new update to igv-reports that supposedly enables usage of .tsv or .maf files, need to check that out as well
There is already a CWL and operator for IGV Reports, need to integrate it into the workflow somewhere.
It requires bam files and variant input files, so that will be a consideration
Also, it needs a list of regions to use for snapshotting, currently the CWL expects a .vcf sites file. But that is kind of awkward to generate, need to enable options for .bed and/or maf files.
The variant files also currently have to be .vcf, there is a new update to
igv-reportsthat supposedly enables usage of .tsv or .maf files, need to check that out as well