diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index 9ff90cedef8..5d93a688cca 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -95,6 +95,7 @@ workflow Mutect2 { # additional modes and outputs File? realignment_index_bundle String? realignment_extra_args + File? dragstr_model Boolean run_orientation_bias_mixture_model_filter = false Boolean make_bamout = false Boolean compress_vcfs = false @@ -178,6 +179,7 @@ workflow Mutect2 { getpileupsummaries_extra_args = getpileupsummaries_extra_args, variants_for_contamination = variants_for_contamination, variants_for_contamination_idx = variants_for_contamination_idx, + dragstr_model = dragstr_model, make_bamout = make_bamout, run_ob_filter = run_orientation_bias_mixture_model_filter, compress_vcfs = compress_vcfs, @@ -380,6 +382,7 @@ task M2 { File? gga_vcf_idx File? variants_for_contamination File? variants_for_contamination_idx + File? dragstr_model File? gatk_override @@ -459,6 +462,7 @@ task M2 { ~{"-pon " + pon} \ ~{"-L " + intervals} \ ~{"--alleles " + gga_vcf} \ + ~{"--dragstr-params-path " + dragstr_model} \ -O "~{output_vcf}" \ ~{true='--bam-output bamout.bam' false='' make_bamout} \ ~{true='--f1r2-tar-gz f1r2.tar.gz' false='' run_ob_filter} \