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Dockstore.cwl
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Dockstore.cwl
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#!/usr/bin/env cwl-runner
class: CommandLineTool
id: BAMStats
label: BAMStats tool
cwlVersion: v1.0
$namespaces:
dct: http://purl.org/dc/terms/
foaf: http://xmlns.com/foaf/0.1/
doc: |
A Docker container for the BAMStats command. See the [BAMStats](http://bamstats.sourceforge.net/) website for more information.
dct:creator:
'@id': http://orcid.org/0000-0002-7681-6415
foaf:name: Brian O'Connor
foaf:mbox: [email protected]
requirements:
- class: DockerRequirement
dockerPull: quay.io/briandoconnor/dockstore-tool-bamstats:1.25-11
- class: InlineJavascriptRequirement
hints:
- class: ResourceRequirement
coresMin: 1
ramMin: 4092
outdirMin: 512000
description: the process requires at least 4G of RAM
inputs:
bam_input:
type: File
format: http://edamontology.org/format_2572
inputBinding:
position: 2
doc: The BAM file used as input, it must be sorted.
mem_gb:
type: int
default: 4
inputBinding:
position: 1
doc: The memory, in GB, for the reporting tool
outputs:
bamstats_report:
type: File
format: http://edamontology.org/format_3615
outputBinding:
glob: bamstats_report.zip
doc: A zip file that contains the HTML report and various graphics.
baseCommand: [bash, /usr/local/bin/bamstats]