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Updating cwl and yml for intervals and other changes
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
wgs-processing-wf.cwl
diff --git
a/WGS-processing/cwl/wgs-processing-wf.cwl
b/WGS-processing/cwl/wgs-processing-wf.cwl
index 9459a3f619ed86188911f97c5825b2be4ef751e6..8cbcf5ee03b17f7d5800b611fd29a4d69cfcc105 100644
(file)
--- a/
WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/
WGS-processing/cwl/wgs-processing-wf.cwl
@@
-22,6
+22,8
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
+ fullintervallist:
+ type: File
knownsites:
type: File
format: edam:format_3016 # VCF
knownsites:
type: File
format: edam:format_3016 # VCF
@@
-40,7
+42,7
@@
inputs:
label: Function used to create HTML report
headhtml:
type: File
label: Function used to create HTML report
headhtml:
type: File
- format: edam:format_2331
# HTML
+ format: edam:format_2331
# HTML
label: Header for HTML report
tailhtml:
type: File
label: Header for HTML report
tailhtml:
type: File
@@
-56,7
+58,7
@@
outputs:
report:
type: File[]
outputSource: bwamem-gatk-report/report
report:
type: File[]
outputSource: bwamem-gatk-report/report
- format: edam:format_
1964
# HTML
+ format: edam:format_
2331
# HTML
label: ClinVar variant reports
steps:
label: ClinVar variant reports
steps:
@@
-74,6
+76,7
@@
steps:
fastq1: getfastq/fastq1
fastq2: getfastq/fastq2
reference: reference
fastq1: getfastq/fastq1
fastq2: getfastq/fastq2
reference: reference
+ fullintervallist: fullintervallist
sample: getfastq/sample
knownsites: knownsites
scattercount: scattercount
sample: getfastq/sample
knownsites: knownsites
scattercount: scattercount