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Updating yml for formats
[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 e1e54eeef1d39b613f235b7fc4410a9c6414f205..de4a648e8a90cd08a697203e205e931a95be8b1c 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@
-1,17
+1,21
@@
cwlVersion: v1.1
class: Workflow
cwlVersion: v1.1
class: Workflow
-label: Variant calling workflow for
single interval
+label: Variant calling workflow for
given interval
requirements:
requirements:
- - class: SubworkflowFeatureRequirement
+ SubworkflowFeatureRequirement: {}
inputs:
bam:
type: File
inputs:
bam:
type: File
+ format: edam:format_2572 # BAM
+ label: Indexed sorted BAM with labeled duplicates
secondaryFiles:
- .bai
reference:
type: File
secondaryFiles:
- .bai
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
secondaryFiles:
- .amb
- .ann
@@
-20,17
+24,24
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
- sample: string
- knownsites1:
+ sample:
+ type: string
+ label: Sample Name
+ knownsites:
type: File
type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known polymorphic sites for BQSR
secondaryFiles:
- .tbi
intervallist:
type: File
secondaryFiles:
- .tbi
intervallist:
type: File
+ label: Scatter intervals file
outputs:
gvcf:
type: File
outputs:
gvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: Given interval filtered GVCF
outputSource: selectvariants/filteredgvcf
steps:
outputSource: selectvariants/filteredgvcf
steps:
@@
-40,12
+51,12
@@
steps:
bam: bam
reference: reference
sample: sample
bam: bam
reference: reference
sample: sample
- knownsites
1: knownsites1
+ knownsites
: knownsites
intervallist: intervallist
out: [recaltable]
applyBQSR:
run: gatk-applyBSQR-with-interval.cwl
intervallist: intervallist
out: [recaltable]
applyBQSR:
run: gatk-applyBSQR-with-interval.cwl
- in:
+ in:
reference: reference
bam: bam
sample: sample
reference: reference
bam: bam
sample: sample
@@
-62,7
+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
@@
-75,6
+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