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Updating readme and reorganization
[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 c7bd8021f8ed0ad9d9018201e281c2b04dd3c37e..4e9f456b24fec167cc3098a71560395254dd74da 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@
-34,7
+34,7
@@
outputs:
steps:
basecalibrator:
steps:
basecalibrator:
- run:
./helper/
gatk-baserecalibrator-with-interval.cwl
+ run: gatk-baserecalibrator-with-interval.cwl
in:
bam: bam
reference: reference
in:
bam: bam
reference: reference
@@
-43,7
+43,7
@@
steps:
intervallist: intervallist
out: [recaltable]
applyBQSR:
intervallist: intervallist
out: [recaltable]
applyBQSR:
- run:
./helper/
gatk-applyBSQR-with-interval.cwl
+ run: gatk-applyBSQR-with-interval.cwl
in:
reference: reference
bam: bam
in:
reference: reference
bam: bam
@@
-52,7
+52,7
@@
steps:
recaltable: basecalibrator/recaltable
out: [recalbam]
haplotypecaller:
recaltable: basecalibrator/recaltable
out: [recalbam]
haplotypecaller:
- run:
./helper/
gatk-haplotypecaller-with-interval.cwl
+ run: gatk-haplotypecaller-with-interval.cwl
in:
reference: reference
bam: applyBQSR/recalbam
in:
reference: reference
bam: applyBQSR/recalbam
@@
-60,7
+60,7
@@
steps:
intervallist: intervallist
out: [gvcf]
selectvariants:
intervallist: intervallist
out: [gvcf]
selectvariants:
- run:
./helper/
gatk-selectvariants.cwl
+ run: gatk-selectvariants.cwl
in:
gvcf: haplotypecaller/gvcf
reference: reference
in:
gvcf: haplotypecaller/gvcf
reference: reference