- .sa
- .fai
- ^.dict
- sample:
- type: string
- label: Sample name
- knownsites:
+ fullintervallist:
+ type: File
+ knownsites1:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known SNPS sites for BQSR
+ secondaryFiles:
+ - .idx
+ knownsites2:
type: File
format: edam:format_3016 # VCF
- label: VCF of known polymorphic sites for BQSR
+ label: VCF of known indel sites for BQSR
secondaryFiles:
- - .tbi
+ - .tbi
scattercount:
type: string
label: Desired split for variant calling
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:
type: File[]
outputSource: bwamem-gatk-report/gvcf
format: edam:format_3016 # GVCF
- label: GVCFs generated from sets of fastqs
-
+ label: GVCFs generated from GATK
report:
type: File[]
outputSource: bwamem-gatk-report/report
- format: edam:format_1964 # HTML
+ format: edam:format_2331 # HTML
label: ClinVar variant reports
steps:
fastq1: getfastq/fastq1
fastq2: getfastq/fastq2
reference: reference
+ fullintervallist: fullintervallist
sample: getfastq/sample
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
scattercount: scattercount
clinvarvcf: clinvarvcf
reportfunc: reportfunc
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