Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
cwlVersion: v1.1
class: CommandLineTool
cwlVersion: v1.1
class: CommandLineTool
-label: Annotating and Filtering VCF
+label: Annotate and filter VCF
requirements:
- class: DockerRequirement
requirements:
- class: DockerRequirement
type: File
clinvarvcf:
type: File
type: File
clinvarvcf:
type: File
outputs:
reporttxt: stdout
outputs:
reporttxt: stdout
cwlVersion: v1.1
class: CommandLineTool
cwlVersion: v1.1
class: CommandLineTool
-label: Converts gvcf to vcf
+label: Convert GVCF to VCF
requirements:
- class: DockerRequirement
requirements:
- class: DockerRequirement
ResourceRequirement:
ramMin: 10000
coresMin: 4
ResourceRequirement:
ramMin: 10000
coresMin: 4
+ SoftwareRequirement:
+ packages:
+ BCFtools:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_005227" ]
+ version: [ "1.10.2" ]
+ HTSlib:
+ version: [ "1.10.2" ]
+
+ format: edam:format_3016 # GVCF
+ label: GVCF generated from GATK
+ format: edam:format_3016 # VCF
+ label: VCF extracted from GVCF
outputBinding:
glob: "*.vcf.gz"
secondaryFiles: [.tbi]
outputBinding:
glob: "*.vcf.gz"
secondaryFiles: [.tbi]
valueFrom: "AVG(GQ)>20"
- valueFrom: "-Ov"
- prefix: "-o"
valueFrom: "AVG(GQ)>20"
- valueFrom: "-Ov"
- prefix: "-o"
- valueFrom: $(inputs.samplename).vcf
+ valueFrom: $(inputs.sample).vcf
- {valueFrom: '&&', shellQuote: false}
- bgzip
- {valueFrom: '&&', shellQuote: false}
- bgzip
- - valueFrom: $(inputs.samplename).vcf
+ - valueFrom: $(inputs.sample).vcf
- {valueFrom: '&&', shellQuote: false}
- tabix
- {valueFrom: '&&', shellQuote: false}
- tabix
- - valueFrom: $(inputs.samplename).vcf.gz
+ - valueFrom: $(inputs.sample).vcf.gz
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl
type: File
format: edam:format_3016 # GVCF
label: Gathered GVCF
type: File
format: edam:format_3016 # GVCF
label: Gathered GVCF
type: string
label: Sample Name
clinvarvcf:
type: string
label: Sample Name
clinvarvcf:
run: gvcf-to-vcf.cwl
in:
gvcf: gvcf
run: gvcf-to-vcf.cwl
in:
gvcf: gvcf
annotate:
run: annotate-vcf.cwl
in:
vcf: gvcf-to-vcf/vcf
clinvarvcf: clinvarvcf
out: [reporttxt]
annotate:
run: annotate-vcf.cwl
in:
vcf: gvcf-to-vcf/vcf
clinvarvcf: clinvarvcf
out: [reporttxt]
generate-report:
run: generate-report.cwl
in:
generate-report:
run: generate-report.cwl
in: