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Removing white space and commenting out schemas
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
gatk-wf-with-interval.cwl
diff --git
a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
index 38e185d5b67e26f299bb39a4b1419cd5893fd9e8..a5d1993652859aacc0430f982f2b50851336d8ac 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@
-1,6
+1,6
@@
cwlVersion: v1.1
class: Workflow
cwlVersion: v1.1
class: Workflow
-label: Variant calling workflow for given interval
+label: Variant calling workflow for given interval
requirements:
- class: SubworkflowFeatureRequirement
requirements:
- class: SubworkflowFeatureRequirement
@@
-24,7
+24,7
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
- sample:
+ sample:
type: string
label: Sample Name
knownsites:
type: string
label: Sample Name
knownsites:
@@
-35,7
+35,7
@@
inputs:
- .tbi
intervallist:
type: File
- .tbi
intervallist:
type: File
- label: Scatter intervals file
+ label: Scatter intervals file
outputs:
gvcf:
outputs:
gvcf:
@@
-56,7
+56,7
@@
steps:
out: [recaltable]
applyBQSR:
run: gatk-applyBSQR-with-interval.cwl
out: [recaltable]
applyBQSR:
run: gatk-applyBSQR-with-interval.cwl
- in:
+ in:
reference: reference
bam: bam
sample: sample
reference: reference
bam: bam
sample: sample
@@
-73,7
+73,7
@@
steps:
out: [gvcf]
selectvariants:
run: gatk-selectvariants.cwl
out: [gvcf]
selectvariants:
run: gatk-selectvariants.cwl
- in:
+ in:
gvcf: haplotypecaller/gvcf
reference: reference
sample: sample
gvcf: haplotypecaller/gvcf
reference: reference
sample: sample
@@
-86,6
+86,6
@@
$namespaces:
s: https://schema.org/
edam: http://edamontology.org/
s: https://schema.org/
edam: http://edamontology.org/
-$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