fix: tnseq

tasks/TNseq.wdl

@@ -46,21 +46,12 @@ task TNseq {
     $INPUT $INTERVAL \
     --algo TNhaplotyper2 $SAMPLE \
     --dbsnp ${dbsnp_dir}/${dbsnp} \
-    ${sample}.TNseq.raw.vcf \
-    --algo OrientationBias --tumor_sample ${tumor_name} \
-    ${sample}.orientation \
-    --algo ContaminationModel $SAMPLE \
-    --vcf ${germline_resource} \
-    --tumor_segments ${sample}.contamination.segments \
-    ${sample}.contamination
+    ${sample}.TNseq.raw.vcf
     
     sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} \
     --algo TNfilter $SAMPLE \
     -v ${sample}.TNseq.raw.vcf \
-    --contamination ${sample}.contamination \
-    --tumor_segments ${sample}.contamination.segments \
-    --orientation_priors ${sample}.orientation \
     ${sample}.TNseq.vcf
   >>>
   
@@ -74,8 +65,7 @@ task TNseq {
   output {
     File vcf = "${sample}.TNseq.vcf"
     File vcf_index = "${sample}.TNseq.vcf.idx"
-    File contamination = "${sample}.contamination"
-    File contamination_segments = "${sample}.contamination.segments"
-    File orientation = "${sample}.orientation"
+    File raw_vcf = "${sample}.TNseq.raw.vcf"
+    File raw_vcf_index = "${sample}.TNseq.raw.vcf.idx"
   }
 }

workflow.wdl

@@ -340,101 +340,103 @@ workflow {{ project_name }} {
     disk_size=disk_size
   }
   
-  call somatic.somatic as somatic {
-    input:
-    sample=sample_id,
-    normal_bam=normal_BQSR.recaled_bam,
-    normal_bam_index=normal_BQSR.recaled_bam_index,
-    tumor_bam=tumor_BQSR.recaled_bam,
-    tumor_bam_index=tumor_BQSR.recaled_bam_index,
-    ref_dir=ref_dir,
-    fasta=fasta,
-    docker=varscan_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_16cpu_32gb
-  }
-  
-  call processSomatic.processSomatic as processSomatic {
-    input:
-    sample=sample_id,
-    varscan_snp=somatic.varscan_snp,
-    varscan_indel=somatic.varscan_indel,
-    docker=varscan_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_16cpu_32gb
-  }
-  
-  call somaticFilter.somaticFilter as somaticFilter {
-    input:
-    sample=sample_id,
-    varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,
-    varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,
-    varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,
-    varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,
-    varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,
-    varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,
-    varscan_indel=somatic.varscan_indel,
-    docker=varscan_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_16cpu_32gb
-  }
-  
-  call bcftools.bcftools as VarScan_bcftools {
-    input:
-    vcf=somaticFilter.varscan_somatic_filter,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    docker=bcftools_docker,
-    cluster_config=cluster_2cpu_4gb,
-    disk_size=disk_size
-  }
-  
-  call ANNOVAR.ANNOVAR as VarScan_ANNOVAR {
-    input:
-    vcf=VarScan_bcftools.norm_vcf,
-    annovar_database=annovar_database,
-    docker=annovar_docker,
-    cluster_config=cluster_16cpu_32gb,
-    disk_size=disk_size
-  }
-  
-  call TNscope.TNscope as TNscope {
-    input:
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    sample=sample_id,
-    normal_recaled_bam=normal_BQSR.recaled_bam,
-    normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
-    tumor_recaled_bam=tumor_BQSR.recaled_bam,
-    tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
-    normal_name=sample_id + ".N",
-    tumor_name=sample_id + ".T",
-    fasta=fasta,
-    ref_dir=ref_dir,
-    regions=regions,
-    interval_padding=interval_padding,
-    dbsnp=dbsnp,
-    dbsnp_dir=dbsnp_dir,
-    docker=sentieon_docker,
-    cluster_config=cluster_16cpu_32gb,
-    disk_size=disk_size
-  }
-  
-  call bcftools.bcftools as TNscope_bcftools {
-    input:
-    vcf=TNscope.TNscope_vcf,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    docker=bcftools_docker,
-    cluster_config=cluster_2cpu_4gb,
-    disk_size=disk_size
-  }
-  
-  call ANNOVAR.ANNOVAR as TNscope_ANNOVAR {
-    input:
-    vcf=TNscope_bcftools.norm_vcf,
-    annovar_database=annovar_database,
-    docker=annovar_docker,
-    cluster_config=cluster_16cpu_32gb,
-    disk_size=disk_size
+  if (multi_caller){
+    call somatic.somatic as somatic {
+      input:
+      sample=sample_id,
+      normal_bam=normal_BQSR.recaled_bam,
+      normal_bam_index=normal_BQSR.recaled_bam_index,
+      tumor_bam=tumor_BQSR.recaled_bam,
+      tumor_bam_index=tumor_BQSR.recaled_bam_index,
+      ref_dir=ref_dir,
+      fasta=fasta,
+      docker=varscan_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_16cpu_32gb
+    }
+    
+    call processSomatic.processSomatic as processSomatic {
+      input:
+      sample=sample_id,
+      varscan_snp=somatic.varscan_snp,
+      varscan_indel=somatic.varscan_indel,
+      docker=varscan_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_16cpu_32gb
+    }
+    
+    call somaticFilter.somaticFilter as somaticFilter {
+      input:
+      sample=sample_id,
+      varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,
+      varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,
+      varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,
+      varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,
+      varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,
+      varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,
+      varscan_indel=somatic.varscan_indel,
+      docker=varscan_docker,
+      disk_size=disk_size,
+      cluster_config=cluster_16cpu_32gb
+    }
+    
+    call bcftools.bcftools as VarScan_bcftools {
+      input:
+      vcf=somaticFilter.varscan_somatic_filter,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      docker=bcftools_docker,
+      cluster_config=cluster_2cpu_4gb,
+      disk_size=disk_size
+    }
+    
+    call ANNOVAR.ANNOVAR as VarScan_ANNOVAR {
+      input:
+      vcf=VarScan_bcftools.norm_vcf,
+      annovar_database=annovar_database,
+      docker=annovar_docker,
+      cluster_config=cluster_16cpu_32gb,
+      disk_size=disk_size
+    }
+    
+    call TNscope.TNscope as TNscope {
+      input:
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id,
+      normal_recaled_bam=normal_BQSR.recaled_bam,
+      normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+      tumor_recaled_bam=tumor_BQSR.recaled_bam,
+      tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
+      normal_name=sample_id + ".N",
+      tumor_name=sample_id + ".T",
+      fasta=fasta,
+      ref_dir=ref_dir,
+      regions=regions,
+      interval_padding=interval_padding,
+      dbsnp=dbsnp,
+      dbsnp_dir=dbsnp_dir,
+      docker=sentieon_docker,
+      cluster_config=cluster_16cpu_32gb,
+      disk_size=disk_size
+    }
+    
+    call bcftools.bcftools as TNscope_bcftools {
+      input:
+      vcf=TNscope.TNscope_vcf,
+      fasta=fasta,
+      ref_dir=ref_dir,
+      docker=bcftools_docker,
+      cluster_config=cluster_2cpu_4gb,
+      disk_size=disk_size
+    }
+    
+    call ANNOVAR.ANNOVAR as TNscope_ANNOVAR {
+      input:
+      vcf=TNscope_bcftools.norm_vcf,
+      annovar_database=annovar_database,
+      docker=annovar_docker,
+      cluster_config=cluster_16cpu_32gb,
+      disk_size=disk_size
+    }
   }
 }