Updating CWL for overarching workflow

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/cwl/bwa-gatk-wf.cwl b/cwl/bwa-gatk-wf.cwl
index 8069a1d31f3429107b6bffd78ff3e6a70390402a..56c1758f591f1e02dbe3c145333c771ff81a3fd6 100644 (file)
--- a/cwl/bwa-gatk-wf.cwl
+++ b/cwl/bwa-gatk-wf.cwl
@@ -1,6 +1,9 @@
 cwlVersion: v1.1
 class: Workflow
 
+requirements:
+  - class: SubworkflowFeatureRequirement
+
 inputs:
   fastq1: File
   fastq2: File

diff --git a/cwl/fastqc.cwl b/cwl/fastqc.cwl
index 4708aaf8ae75e4ede4d50722a024cdd2871528de..888ba926e5f008e8eb126242a5ea00ccdc6ff9b4 100644 (file)
--- a/cwl/fastqc.cwl
+++ b/cwl/fastqc.cwl
@@ -24,7 +24,7 @@ outputs:
     outputBinding:
       glob: "*fastqc.zip"
 
-basecommand: perl
+baseCommand: perl
 arguments:
   - /FastQC/fastqc
   - $(inputs.fastq1.basename)

diff --git a/cwl/gatk-haplotypecaller.cwl b/cwl/gatk-haplotypecaller.cwl
index 5480eace46b21e2adca91053aeccd5bf8280c41b..ae34a00133dd7993ac201b6344c224c175181e4a 100644 (file)
--- a/cwl/gatk-haplotypecaller.cwl
+++ b/cwl/gatk-haplotypecaller.cwl
@@ -32,10 +32,10 @@ inputs:
   sample: string
 
 outputs:
-  vcf:
+  gvcf:
     type: File
     outputBinding:
-      glob: "*vcf"
+      glob: "*vcf.gz"
 
 arguments:
   - java
@@ -47,6 +47,6 @@ arguments:
   - -I
   - $(inputs.bam)
   - -O
-  - $(runtime.outdir)/$(inputs.sample).gatk.g.vcf
+  - $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
   - -ERC
   - "GVCF"

diff --git a/cwl/samtools-index.cwl b/cwl/samtools-index.cwl
index 3264f95f62e8876f745899d95ddb95f0030a5e61..58ccbf76514879a4967991d7be18702ccd7a76d6 100644 (file)
--- a/cwl/samtools-index.cwl
+++ b/cwl/samtools-index.cwl
@@ -19,7 +19,7 @@ outputs:
     secondaryFiles:
       - .bai
 
-runcommand: samtools
+baseCommand: samtools
 
 arguments:
   - index

diff --git a/cwl/samtools-sort.cwl b/cwl/samtools-sort.cwl
index 8f1f273adbc063596355066c05a3f69d36612c31..cc7c23f0535b4c0124652ea36712779cf84da702 100644 (file)
--- a/cwl/samtools-sort.cwl
+++ b/cwl/samtools-sort.cwl
@@ -17,9 +17,9 @@ outputs:
   out:
     type: File
     outputBinding:
-      glob: "*sorted.bam
+      glob: "*sorted.bam"
 
-runcommand: samtools
+baseCommand: samtools
 
 arguments:
   - sort