8 commit

tasks/starfusion.wdl

 
     command <<<
 	
-    set -o pipefail
-    set -e
+        set -o pipefail
+        set -e
 
-    mkdir -p ${sample_id}/output
+        mkdir -p ${sample_id}/output
 
-    STAR-Fusion --genome_lib_dir ${database_dir} \
-        --left_fq ${fastq1} \
-        --right_fq ${fastq2} \
-        --CPU 4 \
-        --output_dir  ${sample_id}/output
+        STAR-Fusion --genome_lib_dir ${database_dir} \
+            --left_fq ${fastq1} \
+            --right_fq ${fastq2} \
+            --CPU 4 \
+            --output_dir  ${sample_id}/output
     >>>
 	
     runtime {
-    docker : docker
-    cluster: cluster
-    systemDisk: "cloud_ssd 40"
-    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
     }
 
     output {
-    Array[File] starfusion_result=glob("${sample_id}/output/*")
+        Array[File] starfusion_result=glob("${sample_id}/output/*")
     }
 
 }