cwlVersion: v1.1
class: CommandLineTool
-label: Germline variant calling using GATK with output gvcf
-
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
+label: Call variants with GATK HaplotypeCaller
requirements:
DockerRequirement:
ResourceRequirement:
ramMin: 3500
coresMin: 2
+ SoftwareRequirement:
+ packages:
+ GATK:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
+ version: [ "4.1.7" ]
inputs:
bam:
type: File
+ format: edam:format_2572 # BAM
+ label: Recalibrated BAM for given interval
secondaryFiles:
- .bai
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
- ^.dict
intervallist:
type: File
- sample: string
+ label: Scatter intervals file
+ sample:
+ type: string
+ label: Sample Name
outputs:
gvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: GVCF for given interval
secondaryFiles:
- .tbi
outputBinding:
valueFrom: "20"
- prefix: "-GQB"
valueFrom: "60"
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl
cwlVersion: v1.1
class: CommandLineTool
-
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
+label: Filter unused alternates
requirements:
DockerRequirement:
ResourceRequirement:
ramMin: 5000
coresMin: 2
+ SoftwareRequirement:
+ packages:
+ GATK:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
+ version: [ "4.1.7" ]
inputs:
gvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: GVCF for given interval
secondaryFiles:
- .tbi
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
outputs:
filteredgvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: Given interval filtered GVCF
outputBinding:
glob: "*g.vcf.gz"
valueFrom: $(inputs.gvcf.path)
- prefix: "-O"
valueFrom: selected$(inputs.gvcf.basename)
+
+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: Workflow
-label: Variant calling workflow for single interval
+label: Variant calling workflow for given interval
requirements:
- class: SubworkflowFeatureRequirement
gvcf:
type: File
format: edam:format_3016 # GVCF
- label: single interval filtered GVCF
+ label: Given interval filtered GVCF
outputSource: selectvariants/filteredgvcf
steps:
cwlVersion: v1.1
class: Workflow
+label: Report generation workflow
inputs:
gvcf:
cwlVersion: v1.1
class: Workflow
-label: Variant calling workflow scattered over interval splits
+label: Scattered variant calling workflow
requirements:
- class: SubworkflowFeatureRequirement
label: Function used to create HTML report
headhtml:
type: File
- format: edam:format_1964 # HTML
+ format: edam:format_2331# HTML
label: Header for HTML report
tailhtml:
type: File
- format: edam:format_1964 # HTML
+ format: edam:format_2331 # HTML
label: Footer for HTML report
outputs:
class: File
location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
+intervallist:
+ class: File
+ location: keep:4d4947f6637f0acec32580e09d991967+815/0000-scattered.interval_list
bam:
class: File
location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam
+
reference:
class: File
location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+
sample: ERR1726424
+
scattercount: '32'
+
knownsites1:
class: File
location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz