cwlVersion: v1.1
class: CommandLineTool
-label: Germline variant calling using GATK with output gvcf
-
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
+label: Call variants with GATK HaplotypeCaller
requirements:
DockerRequirement:
hints:
arv:RuntimeConstraints:
outputDirType: keep_output_dir
- keep_cache: 1024
+ keep_cache: 1024
ResourceRequirement:
ramMin: 3500
- coresMin: 2
+ coresMin: 2
+ 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: Recalibrated BAM for given interval
secondaryFiles:
- .bai
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
- ^.dict
intervallist:
type: File
- sample: string
+ label: Scatter intervals file
+ sample:
+ type: string
+ label: Sample Name
outputs:
gvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: GVCF for given interval
secondaryFiles:
- .tbi
outputBinding:
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
- valueFrom: $(runtime.outdir)/$(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
+ valueFrom: $(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
- prefix: "-ERC"
valueFrom: "GVCF"
- prefix: "-GQB"
valueFrom: "20"
- prefix: "-GQB"
valueFrom: "60"
+
+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