Fix bug: processSomatic output

tasks/processSomatic.wdl

@@ -21,9 +21,17 @@ 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 = "${sample}.VarScan.TN.SNP.LOH.vcf"
+		File varscan_indel_somatic = "${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_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 = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
 		File varscan_indel_somatic_hc = "${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"
 	}
 }

tasks/somaticFilter.wdl

@@ -2,8 +2,10 @@ task somaticFilter {
     
     String sample
     File varscan_snp_somatic_hc
+    File varscan_snp_germline_hc
     File varscan_snp_loh_hc
     File varscan_indel_somatic_hc
+    File varscan_indel_germline_hc
     File varscan_indel_loh_hc
     File varscan_indel
 
@@ -14,10 +16,14 @@ task somaticFilter {
     command <<<
         java -Xmx12g -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 -Xmx12g -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 -Xmx12g -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 -Xmx12g -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 -Xmx12g -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 -Xmx12g -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
     >>>
 
@@ -30,8 +36,10 @@ task somaticFilter {
 
     output {
 		File varscan_snp_somatic_filter = "${sample}.VarScan.TN.SNP.Somatic.filter.vcf"
+        File varscan_snp_germline_filter = "${sample}.VarScan.TN.SNP.Germline.filter.vcf"
 		File varscan_snp_loh_filter = "${sample}.VarScan.TN.SNP.LOH.filter.vcf"
 		File varscan_indel_somatic_filter = "${sample}.VarScan.TN.INDEL.Somatic.filter.vcf"
+        File varscan_indel_germline_filter = "${sample}.VarScan.TN.INDEL.Germline.filter.vcf"
 		File varscan_indel_loh_filter = "${sample}.VarScan.TN.INDEL.LOH.filter.vcf"
     }
 }

workflow.wdl

@@ -57,8 +57,10 @@ workflow {{ project_name }} {
         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,