test

tasks/batch.wdl

@@ -1,9 +1,9 @@
 task batch {
     String sample_id
-    File tumor_bam
-    File tumor_bai
-    File normal_bam
-    File normal_bai
+    Array[File] tumor_bam
+    Array[File] tumor_bai
+    Array[File] normal_bam
+    Array[File] normal_bai
     String bed
     File ref_dir
     String fasta
@@ -13,13 +13,20 @@ task batch {
 	String disk_size
 
     command <<<
-        cnvkit.py batch ${tumor_bam} --normal ${normal_bam} \
+	    set -o pipefail
+        set -e
+        mkdir -p /cromwell_root/tmp/cnvkit
+		cp ${sep=' ' normal_bai} /cromwell_root/tmp/cnvkit
+        cp ${sep=' ' tumor_bai} /cromwell_root/tmp/cnvkit
+		cd /cromwell_root/tmp/cnvkit
+
+        cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
         --targets ${bed} \
         --fasta ${ref_dir}/${fasta} --access ${access_bed} \
         --output-reference my_reference.cnn --output-dir ./results/ \
         --diagram --scatter
     >>>
-   
+
     runtime { 
 		docker: docker
 		cluster: cluster_config

tasks/export.wdl

@@ -5,9 +5,9 @@ task export{
     String disk_size
 
     command <<<
-		mkdir -p /cromwell_root/tmp/cnvkit_export
-		cp -r ${sep=" " result} /cromwell_root/tmp/cnvkit_export
-		cd /cromwell_root/tmp/cnvkit_export
+		mkdir -p /cromwell_root/tmp/cnvkit
+		cp -r ${sep=" " result} /cromwell_root/tmp/cnvkit
+		cd /cromwell_root/tmp/cnvkit
 		# this version app just provides seg
 		cnvkit.py export seg ./results/*.cns -o samples.seg
     >>>

workflow.wdl

@@ -4,10 +4,10 @@ import "./tasks/export.wdl" as export
 
 workflow {{ project_name }} {	
     String sample_id
-    File tumor_bam
-    File tumor_bai
-    File normal_bam
-    File normal_bai
+    Array[File] tumor_bam
+    Array[File] tumor_bai
+    Array[File] normal_bam
+    Array[File] normal_bai
     String bed
     File ref_dir
     String fasta