cwlVersion: v1.1
class: CommandLineTool
-label: Marking Duplicates using Picard
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
+label: Marking Duplicates using GATK (Picard)
requirements:
DockerRequirement:
coresMin: 4
arv:RuntimeConstraints:
outputDirType: keep_output_dir
+ SoftwareRequirement:
+ packages:
+ GATK:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
+ version: [ "4.1.7" ]
inputs:
bam:
type: File
+ format: edam:format_2572 # BAM
+ label: Sorted BAM
outputs:
dupbam:
type: File
+ format: edam:format_2572 # BAM
+ label: Sorted BAM with labeled duplicates
outputBinding:
glob: "*.bam"
dupmetrics:
type: File
+ label: Duplication metrics file
outputBinding:
glob: "*.txt"
- prefix: "-O"
valueFrom: marked_dups$(inputs.bam.basename)
- prefix: "-M"
- valueFrom: "metrics.txt"
+ valueFrom: "metrics.txt"
+
+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
cwlVersion: v1.1
class: CommandLineTool
-label: Sorting Bam file
-
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
+label: Sorting BAM file
requirements:
DockerRequirement:
arv:RuntimeConstraints:
keep_cache: 9216
outputDirType: keep_output_dir
+ SoftwareRequirement:
+ packages:
+ Samtools:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
+ version: [ "1.10" ]
inputs:
- bam: File
- sample: string
+ bam:
+ type: File
+ format: edam:format_2572 # BAM
+ label: Alignments in BAM format
+ sample:
+ type: string
+ label: Sample Name
outputs:
sortedbam:
type: File
+ format: edam:format_2572 # BAM
+ label: Sorted BAM
outputBinding:
glob: "*sorted.bam"
- '2G'
- -o
- $(inputs.sample).sorted.bam
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$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