refactor: varscan

tasks/TNseq.wdl

@@ -70,6 +70,8 @@ task TNseq {
   }
   
   output {
+    File raw_vcf = "${sample}.TNseq.raw.vcf"
+    File raw_vcf_index = "${sample}.TNseq.raw.vcf.idx"
     File vcf = "${sample}.TNseq.vcf"
     File vcf_index = "${sample}.TNseq.vcf.idx"
     File contamination = "${sample}.contamination"

tasks/VarScan.wdl

@@ -0,0 +1,51 @@
+task VarScan {
+
+  String sample
+  File normal_bam
+  File normal_bam_index
+  File tumor_bam
+  File tumor_bam_index
+
+  File ref_dir
+  String fasta
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    # somatic
+    samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx64g -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
+
+    # processSomatic
+    java -Xmx64g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.SNP.vcf
+    java -Xmx64g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.INDEL.vcf
+
+    # somaticFilter
+    java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.SNP.Somatic.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${sample}.VarScan.INDEL.vcf --output-file ${sample}.VarScan.SNP.Somatic.filter.vcf
+    java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.SNP.Germline.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${sample}.VarScan.INDEL.vcf --output-file ${sample}.VarScan.SNP.Germline.filter.vcf
+    java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.SNP.LOH.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${sample}.VarScan.INDEL.vcf --output-file ${sample}.VarScan.SNP.LOH.filter.vcf
+    java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.INDEL.Somatic.hc.vcf --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 -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.INDEL.Germline.hc.vcf --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 -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.INDEL.LOH.hc.vcf --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.SNP.Somatic.filter.vcf | cat ${sample}.VarScan.INDEL.Somatic.filter.vcf - > ${sample}.VarScan.Somatic.vcf
+    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Germline.filter.vcf | cat ${sample}.VarScan.INDEL.Germline.filter.vcf - > ${sample}.VarScan.Germline.vcf
+    awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.LOH.filter.vcf | cat ${sample}.VarScan.INDEL.LOH.filter.vcf - > ${sample}.VarScan.LOH.vcf
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File varscan_snp = "${sample}.VarScan.SNP.vcf"
+    File varscan_indel = "${sample}.VarScan.INDEL.vcf"
+		File varscan_somatic = "${sample}.VarScan.Somatic.vcf"
+    File varscan_germline = "${sample}.VarScan.Germline.vcf"
+		File varscan_loh = "${sample}.VarScan.LOH.vcf"
+  }
+}

tasks/processSomatic.wdl

@@ -1,40 +0,0 @@
-task processSomatic {
-  
-  String sample
-  File varscan_snp
-  File varscan_indel
-  
-  String docker
-  String cluster_config
-  String disk_size
-
-  command <<<
-    cp ${varscan_snp} ./
-    cp ${varscan_indel} ./
-    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.SNP.vcf
-    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.INDEL.vcf
-
-  >>>
-
-  runtime {
-    docker: docker
-    cluster: cluster_config
-    systemDisk: "cloud_ssd 40"
-    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-  }
-
-  output {
-    File varscan_snp_somatic = "${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

@@ -1,31 +0,0 @@
-task somatic {
-
-  String sample
-  File normal_bam
-  File normal_bam_index
-  File tumor_bam
-  File tumor_bam_index
-
-  File ref_dir
-  String fasta  
-  String docker
-  String cluster_config
-  String disk_size
-
-  command <<<
-    samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx32g -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 ${sample}.VarScan.INDEL --strand-filter 1
-  >>>
-
-  runtime {
-    docker: docker
-    cluster: cluster_config
-    systemDisk: "cloud_ssd 40"
-    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-  }
-  
-  output {
-    File varscan_snp = "${sample}.VarScan.SNP.vcf"
-    File varscan_indel = "${sample}.VarScan.INDEL.vcf"
-    
-  }
-}

tasks/somaticFilter.wdl

@@ -1,47 +0,0 @@
-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
-
-  String docker
-  String cluster_config
-  String disk_size
-
-  command <<<
-    java -Xmx32g -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 -Xmx32g -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 -Xmx32g -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 -Xmx32g -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 -Xmx32g -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 -Xmx32g -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.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 - > ${sample}.VarScan.LOH.filter.vcf
-  >>>
-
-  runtime {
-    docker: docker
-    cluster: cluster_config
-    systemDisk: "cloud_ssd 40"
-    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-  }
-
-  output {
-		File varscan_somatic_filter = "${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

@@ -19,9 +19,8 @@ import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/qualimap.wdl" as qualimap
 
 import "./tasks/TNscope.wdl" as TNscope
-import "./tasks/somatic.wdl" as somatic
-import "./tasks/processSomatic.wdl" as processSomatic
-import "./tasks/somaticFilter.wdl" as somaticFilter
+import "./tasks/VarScan.wdl" as VarScan
+
 
 workflow {{ project_name }} {
   
@@ -447,8 +446,7 @@ workflow {{ project_name }} {
     disk_size=disk_size
   }
   
-  
-  call somatic.somatic as somatic {
+  call VarScan.VarScan as VarScan {
     input:
     sample=sample_id,
     normal_bam=normal_BQSR.recaled_bam,
@@ -462,34 +460,9 @@ workflow {{ project_name }} {
     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,
+    vcf=VarScan.varscan_somatic,
     fasta=fasta,
     ref_dir=ref_dir,
     docker=bcftools_docker,