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Updating readme and reorganization
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
report-wf.cwl
diff --git
a/WGS-processing/cwl/helper/report-wf.cwl
b/WGS-processing/cwl/helper/report-wf.cwl
index 3403ebbe7dfb880d5a5d44b8c7a05c5c1c6a6d36..de8ab3f67ce9b20bfd392a1ce31c2300926a00a6 100644
(file)
--- a/
WGS-processing/cwl/helper/report-wf.cwl
+++ b/
WGS-processing/cwl/helper/report-wf.cwl
@@
-22,21
+22,21
@@
outputs:
steps:
gvcf-to-vcf:
steps:
gvcf-to-vcf:
- run:
./helper/
gvcf-to-vcf.cwl
+ run: gvcf-to-vcf.cwl
in:
gvcf: gvcf
samplename: samplename
out: [vcf]
annotate:
in:
gvcf: gvcf
samplename: samplename
out: [vcf]
annotate:
- run:
./helper/
annotate-vcf.cwl
+ run: annotate-vcf.cwl
in:
vcf: gvcf-to-vcf/vcf
clinvarvcf: clinvarvcf
out: [reporttxt]
generate-report:
in:
vcf: gvcf-to-vcf/vcf
clinvarvcf: clinvarvcf
out: [reporttxt]
generate-report:
- run:
./helper/
generate-report.cwl
+ run: generate-report.cwl
in:
reportfunc: reportfunc
sampletxt: annotate/reporttxt
in:
reportfunc: reportfunc
sampletxt: annotate/reporttxt