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Updating cwl and yml for intervals and other changes
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
bwamem-gatk-report-wf.cwl
diff --git
a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
index 522bd822cdbd7178a9c1f8ee9028ca0a5cf86137..dbb1d5024731aa1923fa539217264e6a7070600c 100644
(file)
--- a/
WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/
WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@
-26,6
+26,9
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
+ fullintervallist:
+ type: File
+ label: Full list of intervals to operate over
sample:
type: string
label: Sample Name
sample:
type: string
label: Sample Name
@@
-110,6
+113,7
@@
steps:
run: scatter-gatk-wf-with-interval.cwl
in:
reference: reference
run: scatter-gatk-wf-with-interval.cwl
in:
reference: reference
+ fullintervallist: fullintervallist
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount