style(Manta, MSIsensor): tab

tasks/MSIsensor.wdl

@@ -18,7 +18,7 @@ task MSIsensor {
     nt=$(nproc)
     
     # MSI
-		mkdir -p /cromwell_root/tmp/
+    mkdir -p /cromwell_root/tmp/
     msisensor-pro scan -d ${ref_dir}/${fasta} -o reference.list
     if [ ${normal_bam} ]; then
       msisensor-pro msi -d reference.list -n ${normal_bam} -t ${tumor_bam} -o /cromwell_root/tmp/${sample}

tasks/Manta.wdl

@@ -1,25 +1,25 @@
 task Manta {
   
   File ref_dir
-	File fasta
+  File fasta
   File regions
   File tumor_bam
   File tumor_bam_index
   File? normal_bam
   File? normal_bam_index
-	String sample
-	String docker
-	String cluster_config
-	String disk_size
+  String sample
+  String docker
+  String cluster_config
+  String disk_size
   
-	command <<<
+  command <<<
     set -o pipefail
     set -e
-		nt=$(nproc)
+    nt=$(nproc)
     
     MANTA_INSTALL_PATH="/opt/manta-1.6.0.centos6_x86_64"
     MANTA_ANALYSIS_PATH="/cromwell_root/tmp"
-		mkdir -p $MANTA_ANALYSIS_PATH
+    mkdir -p $MANTA_ANALYSIS_PATH
     
     cp ${regions} my_baits.bed
     bgzip -c my_baits.bed > my_baits.bed.gz
@@ -45,17 +45,17 @@ task Manta {
     else
       cp $MANTA_ANALYSIS_PATH/results/variants/tumorSV.vcf.gz ${sample}.Manta.somaticSV.vcf.gz
     fi
-	>>>
+  >>>
   
-	runtime {
-		docker:docker
+  runtime {
+    docker:docker
     cluster: cluster_config
     systemDisk: "cloud_ssd 40"
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
+  }
   
-	output {
-		File somatic_vcf = "${sample}.Manta.somaticSV.vcf.gz"
-		File? germline_vcf = "${sample}.Manta.germlineSV.vcf.gz"
-	}
+  output {
+    File somatic_vcf = "${sample}.Manta.somaticSV.vcf.gz"
+    File? germline_vcf = "${sample}.Manta.germlineSV.vcf.gz"
+  }
 }