working on param for memory

Author: briandoconnor

Dockstore.cwl

@@ -23,19 +23,19 @@ hints:
     description: "the process requires at least 4G of RAM"
 
 inputs:
-  - id: "#bam_input"
-    type: File
-    description: "The BAM file used as input, it must be sorted."
+  - id: "#mem_gb"
+    type: int
+    default: 4
+    description: "The memory, in GB, for the reporting tool"
     inputBinding:
       position: 1
 
 inputs:
-  - id: "#mem_gb"
+  - id: "#bam_input"
     type: File
-    description: "The memory, in GB, for the reporting tool"
+    description: "The BAM file used as input, it must be sorted."
     inputBinding:
-      position: 1
-
+      position: 2
 
 outputs:
   - id: "#bamstats_report"

bin/bamstats

@@ -1,5 +1,5 @@
 #!/bin/bash
 set -euf -o pipefail
 
-java -Xmx$2g -jar /opt/BAMStats-1.25/BAMStats-1.25.jar -i $1 -o bamstats_report.html -v html
+java -Xmx$1g -jar /opt/BAMStats-1.25/BAMStats-1.25.jar -i $2 -o bamstats_report.html -v html
 zip -r bamstats_report.zip bamstats_report.html bamstats_report.html.data