update wdl to version 1.0 (CancerCollaboratory#8)

* update wdl to version 1.0
dockstore · Sep 13, 2019 · a629508 · a629508
1 parent 50cf2c4
commit a629508
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Showing 3 changed files with 14 additions and 8 deletions.
diff --git a/Dockstore.wdl b/Dockstore.wdl
@@ -1,6 +1,10 @@
+version 1.0
 task bamstats {
-	File bam_input
-	Int mem_gb
+    input {
+        File bam_input
+        Int mem_gb
+    }
+
 
 	command {
 		bash /usr/local/bin/bamstats ${mem_gb} ${bam_input}
@@ -11,7 +15,7 @@ task bamstats {
 	}
 
 	runtime {
-		docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0" 
+		docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0"
 		memory: mem_gb + "GB"
 	}
 
@@ -21,7 +25,9 @@ task bamstats {
 }
 
 workflow bamstatsWorkflow {
-	File bam_input
-	Int mem_gb	
+    input {
+        File bam_input
+        Int mem_gb
+    }
 	call bamstats { input: bam_input=bam_input, mem_gb=mem_gb }
 }
diff --git a/install.sh b/install.sh
@@ -8,8 +8,8 @@ set -o xtrace
 if [[ "${LANGUAGE}" == "cwl" ]]; then
     pip2.7 install --user cwl-runner cwltool==1.0.20160712154127 schema-salad==1.14.20160708181155 avro==1.8.1
 elif [[ "${LANGUAGE}" == "wdl" ]]; then
-    wget https://github.com/broadinstitute/cromwell/releases/download/32/cromwell-32.jar
+    wget https://github.com/broadinstitute/cromwell/releases/download/44/cromwell-44.jar
 elif [[ "${LANGUAGE}" == "nfl" ]]; then
     curl -s https://get.nextflow.io | bash
     mv nextflow $HOME/bin
-fi
+fi
diff --git a/script.sh b/script.sh
@@ -11,7 +11,7 @@ if [[ "${LANGUAGE}" == "cwl" ]]; then
     mv NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam /tmp/
     cwltool --non-strict Dockstore.cwl sample_configs.local.json
 elif [[ "${LANGUAGE}" == "wdl" ]]; then
-    java -jar cromwell-32.jar run Dockstore.wdl --inputs test.wdl.json
+    java -jar cromwell-44.jar run Dockstore.wdl --inputs test.wdl.json
 elif [[ "${LANGUAGE}" == "nfl" ]]; then
     nextflow run main.nf
 fi