Updating readme and reorganization

[arvados-tutorial.git] / WGS-processing / cwl / wgs-processing-wf.cwl

diff --git a/WGS-processing/cwl/wgs-processing-wf.cwl b/WGS-processing/cwl/wgs-processing-wf.cwl
index e43bfe5e95a08d89e2f8a033505abe3ead69366d..9d20a0e23720b28526cb5471ba6131da4fda27d1 100644 (file)
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -1,4 +1,4 @@
-Version: v1.1
+cwlVersion: v1.1
 class: Workflow
 
 requirements:
@@ -41,17 +41,17 @@ steps:
     run: ./helper/getfastq.cwl
     in:
       fastqdir: fastqdir
-    out: [fastq1, fastq2]
+    out: [fastq1, fastq2, sample]
 
   bwamem-gatk-report:
     run: ./helper/bwamem-gatk-report-wf.cwl
-    scatter: [fastq1, fastq2]
+    scatter: [fastq1, fastq2, sample]
     scatterMethod: dotproduct
     in:
       fastq1: getfastq/fastq1
       fastq2: getfastq/fastq2
       reference: reference
-      sample: sample
+      sample: getfastq/sample
       knownsites: knownsites
       scattercount: scattercount
       clinvarvcf: clinvarvcf