- class: 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
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
- knownsites1: knownsites
+ knownsites: knownsites
out: [gatheredgvcf]
generate-report:
run: report-wf.cwl
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