cwlVersion: v1.1
class: CommandLineTool
-label: Indexing Bam File
-
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
+label: Index BAM
requirements:
DockerRequirement:
hints:
arv:RuntimeConstraints:
outputDirType: keep_output_dir
+ SoftwareRequirement:
+ packages:
+ Samtools:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
+ version: [ "1.10" ]
inputs:
- bam: File
+ bam:
+ type: File
+ format: edam:format_2572 # BAM
+ label: Sorted BAM with labeled duplicates
outputs:
indexedbam:
type: File
+ format: edam:format_2572 # BAM
+ label: Indexed sorted BAM with labeled duplicates
outputBinding:
glob: "*bam"
secondaryFiles:
- - .bai
+ - .bai
baseCommand: samtools
arguments:
- index
- $(inputs.bam.basename)
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl