diff --git a/modules/local/pave/somatic/main.nf b/modules/local/pave/somatic/main.nf index 7ad70200..dfecf48c 100644 --- a/modules/local/pave/somatic/main.nf +++ b/modules/local/pave/somatic/main.nf @@ -48,7 +48,6 @@ process PAVE_SOMATIC { // Targeted mode def pon_artefact_arg = pon_artefacts ? "-pon_artefact_file ${pon_artefacts}" : '' - def pathogenic_pass_force_arg = pon_artefacts ? '-force_pathogenic_pass': '' def sage_blocklist_regions_arg = sage_blocklist_regions ? "-blacklist_bed ${sage_blocklist_regions}" : '' def sage_blocklist_sites_arg = sage_blocklist_sites ? "-blacklist_vcf ${sage_blocklist_sites}" : '' def clinvar_annotations = clinvar_annotations ? "-clinvar_vcf ${clinvar_annotations}" : '' @@ -69,7 +68,6 @@ process PAVE_SOMATIC { -ensembl_data_dir ${ensembl_data_resources} \\ ${sage_blocklist_regions_arg} \\ ${sage_blocklist_sites_arg} \\ - ${pathogenic_pass_force_arg} \\ ${gnomad_args} \\ -read_pass_only \\ -threads ${task.cpus} \\