update workflow

tasks/processSomatic.wdl

@@ -11,8 +11,8 @@ task processSomatic {
   command <<<
     cp ${varscan_snp} ./
     cp ${varscan_indel} ./
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.SNP.vcf
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.INDEL.vcf
+    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.SNP.vcf
+    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.INDEL.vcf
 
   >>>
 
@@ -24,17 +24,17 @@ task processSomatic {
   }
 
   output {
-    File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"
-    File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"
-    File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"
-    File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
-    File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"
-    File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
-    File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"
-    File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"
-    File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"
-    File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
-    File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"
-    File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
+    File varscan_snp_somatic = "${sample}.VarScan.SNP.Somatic.vcf"
+    File varscan_snp_germline = "${sample}.VarScan.SNP.Germline.vcf"
+    File varscan_snp_loh = "${sample}.VarScan.SNP.LOH.vcf"
+    File varscan_snp_somatic_hc = "${sample}.VarScan.SNP.Somatic.hc.vcf"
+    File varscan_snp_germline_hc = "${sample}.VarScan.SNP.Germline.hc.vcf"
+    File varscan_snp_loh_hc = "${sample}.VarScan.SNP.LOH.hc.vcf"
+    File varscan_indel_somatic = "${sample}.VarScan.INDEL.Somatic.vcf"
+    File varscan_indel_germline = "${sample}.VarScan.INDEL.Germline.vcf"
+    File varscan_indel_loh = "${sample}.VarScan.INDEL.LOH.vcf"
+    File varscan_indel_somatic_hc = "${sample}.VarScan.INDEL.Somatic.hc.vcf"
+    File varscan_indel_germline_hc = "${sample}.VarScan.INDEL.Germline.hc.vcf"
+    File varscan_indel_loh_hc = "${sample}.VarScan.INDEL.LOH.hc.vcf"
   }
 }

tasks/somatic.wdl

@@ -13,7 +13,7 @@ task somatic {
   String disk_size
 
   command <<<
-    samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1
+    samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.SNP --output-indel ${sample}.VarScan.INDEL --strand-filter 1
   >>>
 
   runtime {
@@ -24,8 +24,8 @@ task somatic {
   }
   
   output {
-    File varscan_snp = "${sample}.VarScan.TN.SNP.vcf"
-    File varscan_indel = "${sample}.VarScan.TN.INDEL.vcf"
+    File varscan_snp = "${sample}.VarScan.SNP.vcf"
+    File varscan_indel = "${sample}.VarScan.INDEL.vcf"
     
   }
 }

tasks/somaticFilter.wdl

@@ -14,22 +14,22 @@ task somaticFilter {
   String disk_size
 
   command <<<
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Somatic.filter.vcf
+    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Somatic.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Germline.filter.vcf
+    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Germline.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.LOH.filter.vcf
+    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.LOH.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf
+    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Somatic.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Germline.filter.vcf
+    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Germline.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.LOH.filter.vcf
+    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.LOH.filter.vcf
 
     # Merge SNP and INDEL
-    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.Somatic.filter.vcf | cat ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf - > ${sample}.VarScan.TN.Somatic.filter.vcf
-    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.Germline.filter.vcf | cat ${sample}.VarScan.TN.INDEL.Germline.filter.vcf - > ${sample}.VarScan.TN.Germline.filter.vcf
-    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.LOH.filter.vcf | cat ${sample}.VarScan.TN.INDEL.LOH.filter.vcf - > ${sample}.VarScan.TN.LOH.filter.vcf
+    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Somatic.filter.vcf | cat ${sample}.VarScan.INDEL.Somatic.filter.vcf - > ${sample}.VarScan.Somatic.filter.vcf
+    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Germline.filter.vcf | cat ${sample}.VarScan.INDEL.Germline.filter.vcf - > ${sample}.VarScan.Germline.filter.vcf
+    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.LOH.filter.vcf | cat ${sample}.VarScan.INDEL.LOH.filter.vcf - > ${sample}.VarScan.LOH.filter.vcf
   >>>
 
   runtime {
@@ -40,8 +40,8 @@ task somaticFilter {
   }
 
   output {
-		File varscan_somatic_filter = "${sample}.VarScan.TN.Somatic.filter.vcf"
-    File varscan_germline_filter = "${sample}.VarScan.TN.Germline.filter.vcf"
-		File varscan_loh_filter = "${sample}.VarScan.TN.LOH.filter.vcf"
+		File varscan_somatic_filter = "${sample}.VarScan.Somatic.filter.vcf"
+    File varscan_germline_filter = "${sample}.VarScan.Germline.filter.vcf"
+		File varscan_loh_filter = "${sample}.VarScan.LOH.filter.vcf"
   }
 }

workflow.wdl

@@ -232,7 +232,7 @@ workflow {{ project_name }} {
         input:
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
-        sample=sample_id + '.N',
+        sample=sample_id,
         fasta=fasta,
         ref_dir=ref_dir,
         recaled_bam=normal_BQSR.recaled_bam,
@@ -249,7 +249,7 @@ workflow {{ project_name }} {
     if (pindel) {
       call Pindel.Pindel as Pindel {
         input:	
-        sample_id=sample_id + '.N',
+        sample_id=sample_id,
         bam=normal_BQSR.recaled_bam,
         bam_index=normal_BQSR.recaled_bam_index,
         fasta=fasta,
@@ -378,7 +378,7 @@ workflow {{ project_name }} {
       }
     }
 
-    if (varscan) {
+    if (varscan && normal_fastq_1 != "") {
       call somatic.somatic as somatic {
         input:
         sample=sample_id,
@@ -522,7 +522,7 @@ workflow {{ project_name }} {
         input:
         SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
         SENTIEON_LICENSE=SENTIEON_LICENSE,
-        sample=sample_id + '.N',
+        sample=sample_id,
         fasta=fasta,
         ref_dir=ref_dir,
         recaled_bam=normal_BQSR_fb.recaled_bam,
@@ -538,8 +538,8 @@ workflow {{ project_name }} {
 
     if (pindel) {
       call Pindel.Pindel as Pindel_fb {
-        input:	
-        sample_id=sample_id + '.N',
+        input:
+        sample_id=sample_id,
         bam=normal_BQSR_fb.recaled_bam,
         bam_index=normal_BQSR_fb.recaled_bam_index,
         fasta=fasta,