second commit

tasks/starfusion.wdl

 task starfusion{
-	String sample_id
-	File fastq1
-	File fastq2
-	File database_dir
+    String sample_id
+    File fastq1
+    File fastq2
+    File database_dir
 	
-	String docker
-	String cluster
-	String disk_size
+    String docker
+    String cluster
+    String disk_size
 
-	command <<<
+    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} \
+    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/"
-	}
+    runtime {
+    docker :  docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
 
-	output {
-	Array[File] starfusion_result=glob("${sample_id}/output/*")
-	}
+    output {
+    Array[File] starfusion_result=glob("${sample_id}/output/*")
+    }
 
 }
 

workflow.wdl

 import "./tasks/starfusion.wdl" as starfusion
 workflow {{project_name}} {
-	String sample_id
-        File fastq1
-        File fastq2
-        File starfusion_database_dir
+    String sample_id
+    File fastq1
+    File fastq2
+    File starfusion_database_dir
 
-        String starfusion_docker
-	String starfusion_cluster
-	String disk_size
+    String starfusion_docker
+    String starfusion_cluster
+    String disk_size
 
-	call starfusion.starfusion as starfusion {
-	input:	
-	sample_id=sample_id,
-	fastq1=fastq1,
-	fastq2=fastq2,
-	database_dir=starfusion_database_dir,
-	docker=starfusion_docker,
-	cluster = starfusion_cluster,
-	disk_size = disk_size
+        call starfusion.starfusion as starfusion {
+                input:	
+                sample_id=sample_id,
+                fastq1=fastq1,
+                fastq2=fastq2,
+                database_dir=starfusion_database_dir,
+                docker=starfusion_docker,
+                cluster = starfusion_cluster,
+                disk_size = disk_size
 
-	}
+        }
 
 
 }