cwlVersion: v1.1
class: Workflow
+label: WGS processing workflow scattered over samples
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
inputs:
- fastqdir: Directory
+ fastqdir:
+ type: Directory
+ label: Directory of paired FASTQ files
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
- .sa
- .fai
- ^.dict
- sample: string
knownsites:
type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known polymorphic sites for BQSR
secondaryFiles:
- .tbi
- scattercount: string
- clinvarvcf: File
- reportfunc: File
- headhtml: File
- tailhtml: File
+ scattercount:
+ type: string
+ label: Desired split for variant calling
+ clinvarvcf:
+ type: File
+ format: edam:format_3016 # VCF
+ label: Reference VCF for ClinVar
+ reportfunc:
+ type: File
+ label: Function used to create HTML report
+ headhtml:
+ type: File
+ format: edam:format_2331# HTML
+ label: Header for HTML report
+ tailhtml:
+ type: File
+ format: edam:format_2331 # HTML
+ label: Footer for HTML report
outputs:
gvcf:
type: File[]
outputSource: bwamem-gatk-report/gvcf
+ format: edam:format_3016 # GVCF
+ label: GVCFs generated from GATK
report:
type: File[]
outputSource: bwamem-gatk-report/report
+ format: edam:format_1964 # HTML
+ label: ClinVar variant reports
steps:
getfastq:
run: ./helper/getfastq.cwl
in:
fastqdir: fastqdir
- out: [fastq1, fastq2]
+ out: [fastq1, fastq2, sample]
bwamem-gatk-report:
run: ./helper/bwamem-gatk-report-wf.cwl
- scatter: [fastq1, fastq2]
+ scatter: [fastq1, fastq2, sample]
scatterMethod: dotproduct
in:
fastq1: getfastq/fastq1
fastq2: getfastq/fastq2
reference: reference
- sample: sample
+ sample: getfastq/sample
knownsites: knownsites
scattercount: scattercount
clinvarvcf: clinvarvcf
headhtml: headhtml
tailhtml: tailhtml
out: [qc-html,qc-zip,gvcf,report]
+
+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