Update 'workflow.wdl'

workflow.wdl

@@ -459,24 +459,6 @@ workflow {{ project_name }} {
         disk_size=disk_size,
         cluster_config=cluster_config
       }
-
-      call BQSR.BQSR as tumor_BQSR_fb {
-        input:
-        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-        SENTIEON_LICENSE=SENTIEON_LICENSE,
-        fasta=fasta,
-        ref_dir=ref_dir,
-        deduped_bam=tumor_replaceRG.deduped_bam,
-        deduped_bam_index=tumor_replaceRG.deduped_bam_index,
-        db_mills=db_mills,
-        dbmills_dir=dbmills_dir,
-        dbsnp=dbsnp,
-        dbsnp_dir=dbsnp_dir,
-        sample=sample_id + '.T',
-        docker=sentieon_docker,
-        disk_size=disk_size,
-        cluster_config=cluster_config
-      }
     }
     
     if (normal_deduped_bam != "") {
@@ -490,24 +472,6 @@ workflow {{ project_name }} {
         disk_size=disk_size,
         cluster_config=cluster_config
       }
-
-      call BQSR.BQSR as normal_BQSR_fb {
-        input:
-        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-        SENTIEON_LICENSE=SENTIEON_LICENSE,
-        fasta=fasta,
-        ref_dir=ref_dir,
-        deduped_bam=normal_replaceRG.deduped_bam,
-        deduped_bam_index=normal_replaceRG.deduped_bam_index,
-        db_mills=db_mills,
-        dbmills_dir=dbmills_dir,
-        dbsnp=dbsnp,
-        dbsnp_dir=dbsnp_dir,
-        sample=sample_id + '.N',
-        docker=sentieon_docker,
-        disk_size=disk_size,
-        cluster_config=cluster_config
-      }
     }
     
     if (haplotyper) {