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Merge branch 'release/1.25-2'
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briandoconnor committed Nov 3, 2015
2 parents 1d20c4e + 95f8274 commit c27b3dc
Showing 2 changed files with 11 additions and 3 deletions.
12 changes: 10 additions & 2 deletions Dockstore.cwl
Original file line number Diff line number Diff line change
@@ -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"
2 changes: 1 addition & 1 deletion bin/bamstats
Original file line number Diff line number Diff line change
@@ -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

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