Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
class: CommandLineTool
label: Apply base quality score recalibration
class: CommandLineTool
label: Apply base quality score recalibration
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
-
requirements:
DockerRequirement:
dockerPull: broadinstitute/gatk:4.1.7.0
requirements:
DockerRequirement:
dockerPull: broadinstitute/gatk:4.1.7.0
ResourceRequirement:
ramMin: 5000
coresMin: 2
ResourceRequirement:
ramMin: 5000
coresMin: 2
+ SoftwareRequirement:
+ packages:
+ GATK:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
+ version: [ "4.1.7" ]
+ format: edam:format_2572 # BAM
+ label: Indexed sorted BAM with labeled duplicates
secondaryFiles:
- .bai
reference:
type: File
secondaryFiles:
- .bai
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
secondaryFiles:
- .amb
- .ann
+ sample:
+ type: string
+ label: Sample Name
+ label: Recalibration table
+ label: Scatter intervals file
outputs:
recalbam:
type: File
outputs:
recalbam:
type: File
+ format: edam:format_2572 # BAM
+ label: Recalibrated BAM for given interval
secondaryFiles:
- .bai
outputBinding:
secondaryFiles:
- .bai
outputBinding:
valueFrom: $(inputs.intervallist)
- prefix: "-O"
valueFrom: $(inputs.sample)nodups_BQSR.bam
valueFrom: $(inputs.intervallist)
- prefix: "-O"
valueFrom: $(inputs.sample)nodups_BQSR.bam
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$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
outputs:
recaltable:
type: File
outputs:
recaltable:
type: File
- label: Recalibration table
+ label: Recalibration table for given interval
outputBinding:
glob: "*.table"
outputBinding:
glob: "*.table"