cwlVersion: v1.1
class: CommandLineTool
-label: Generating recalibration table for BQSR
-
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
+label: Generate recalibration table for BQSR
requirements:
DockerRequirement:
ResourceRequirement:
ramMin: 5000
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: Indexed sorted BAM with labeled duplicates
secondaryFiles:
- .bai
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
- .sa
- .fai
- ^.dict
- sample: string
+ sample:
+ type: string
+ label: Sample Name
knownsites1:
type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known polymorphic sites for BQSR
secondaryFiles:
- .tbi
intervallist:
type: File
+ label: Scatter intervals file
outputs:
recaltable:
type: File
+ label: Recalibration table
outputBinding:
glob: "*.table"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
valueFrom: $(inputs.sample)_recal_data.table
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl
inputs:
bam:
type: File
+ format: edam:format_2572 # BAM
+ label: Indexed sorted BAM with labeled duplicates
secondaryFiles:
- .bai
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
- .sa
- .fai
- ^.dict
- sample: string
+ sample:
+ type: string
+ label: Sample Name
knownsites1:
type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known polymorphic sites for BQSR
secondaryFiles:
- .tbi
intervallist:
type: File
+ label: Scatter intervals file
outputs:
gvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: single interval filtered GVCF
outputSource: selectvariants/filteredgvcf
steps: