label: WGS processing workflow for single sample
requirements:
- - class: SubworkflowFeatureRequirement
+ SubworkflowFeatureRequirement: {}
inputs:
- fastq1:
+ fastq1:
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R1)
- fastq2:
+ fastq2:
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R2)
sample: sample
out: [bam]
samtools-sort:
- run: samtools-sort.cwl
+ run: samtools-sort.cwl
in:
bam: bwamem-samtools-view/bam
sample: sample
run: report-wf.cwl
in:
gvcf: haplotypecaller/gatheredgvcf
- samplename: sample
+ sample: sample
clinvarvcf: clinvarvcf
reportfunc: reportfunc
headhtml: headhtml
tailhtml: tailhtml
- out: [report]
+ out: [report]
s:codeRepository: https://github.com/arvados/arvados-tutorial
s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
s: https://schema.org/
edam: http://edamontology.org/
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl