Merge branch 'release/1.25-2'

Author: briandoconnor

Dockstore.cwl

@@ -12,7 +12,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/briandoconnor/dockstore-tool-bamstats:1.25"
+    dockerPull: "quay.io/briandoconnor/dockstore-tool-bamstats:1.25-1"
   - { import: node-engine.cwl }
 
 hints:
@@ -22,12 +22,20 @@ hints:
     outdirMin: 512000
     description: "the process requires at least 4G of RAM"
 
+inputs:
+  - id: "#mem_gb"
+    type: int
+    default: 4
+    description: "The memory, in GB, for the reporting tool"
+    inputBinding:
+      position: 1
+
 inputs:
   - id: "#bam_input"
     type: File
     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 -Xmx4g -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