- .sa
- .fai
- ^.dict
+ fullintervallist:
+ type: File
+ label: Full list of intervals to operate over
sample:
type: string
label: Sample Name
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:
qc-html:
type: File[]
label: FASTQ QC reports
- format: edam:format_1964 # HTML
+ format: edam:format_2331 # HTML
outputSource: fastqc/out-html
qc-zip:
type: File[]
report:
type: File
outputSource: generate-report/report
- format: edam:format_1964 # HTML
+ format: edam:format_2331 # HTML
label: ClinVar variant report
steps:
run: scatter-gatk-wf-with-interval.cwl
in:
reference: reference
+ fullintervallist: fullintervallist
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount