third commit

tasks/fusioncatcher.wdl

 task fusioncatcher{
-	String sample_id
-	File sample_fastq_dir
-	File database_dir
+    String sample_id
+    File sample_fastq_dir
+    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
 
 
-	/software/fusioncatcher/bin/fusioncatcher \
-	-d ${database_dir} \
-	-p 4 \
-	--input ${sample_fastq_dir} \
-	--output ${sample_id}/output
+    /software/fusioncatcher/bin/fusioncatcher \
+        -d ${database_dir} \
+        -p 4 \
+        --input ${sample_fastq_dir} \
+        --output ${sample_id}/output
 
-	>>>
+    >>>
 	
-	runtime {
-	docker :  docker
-	cluster: cluster
-	systemDisk: "cloud_ssd 40"
-	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-	Array[File] fusioncatcher_result=glob("${sample_id}/output/*")
-	}
+    runtime {
+    docker :  docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+    Array[File] fusioncatcher_result=glob("${sample_id}/output/*")
+    }
 
 }
 

workflow.wdl

 import "./tasks/fusioncatcher.wdl" as fusioncatcher
 
 workflow {{project_name}} {
-	String sample_id
-        File sample_fastq_dir
-        File fusioncatcher_database_dir
+    String sample_id
+    File sample_fastq_dir
+    File fusioncatcher_database_dir
 
-        String fusioncatcher_docker
-	String	fusioncatcher_cluster
-	String disk_size
+    String fusioncatcher_docker
+    String	fusioncatcher_cluster
+    String disk_size
 
-	call fusioncatcher {
-	input:	
-	sample_id=sample_id,
-	sample_fastq_dir=sample_fastq_dir,
-	database_dir=fusioncatcher_database_dir,
-	docker=fusioncatcher_docker,
-	cluster = fusioncatcher_cluster,
-	disk_size = disk_size
+	    call fusioncatcher.fusioncatcher as fusioncatcher {
+	            input:	
+	            sample_id=sample_id,
+	            sample_fastq_dir=sample_fastq_dir,
+	            database_dir=fusioncatcher_database_dir,
+	            docker=fusioncatcher_docker,
+	            cluster = fusioncatcher_cluster,
+	            disk_size = disk_size
 
-	}
+	    }
 
 
 }