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:
-    run: ./helper/gatk-baserecalibrator-with-interval.cwl
+    run: gatk-baserecalibrator-with-interval.cwl
     in:
       bam: bam
       reference: reference
@@ -43,7 +43,7 @@ steps:
       intervallist: intervallist
     out: [recaltable]
   applyBQSR:
-    run: ./helper/gatk-applyBSQR-with-interval.cwl
+    run: gatk-applyBSQR-with-interval.cwl
     in: 
       reference: reference
       bam: bam
@@ -52,7 +52,7 @@ steps:
       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
@@ -60,7 +60,7 @@ steps:
       intervallist: intervallist
     out: [gvcf]
   selectvariants:
-    run: ./helper/gatk-selectvariants.cwl
+    run: gatk-selectvariants.cwl
     in: 
       gvcf: haplotypecaller/gvcf
       reference: reference