From c5b4f78c29d4daa9aab251181391a688d10b97f3 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Wed, 11 Mar 2020 15:04:04 +0000
Subject: [PATCH] Updating CWL for overarching workflow
 Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com> no issue #

---
 cwl/bwa-gatk-wf.cwl          | 3 +++
 cwl/fastqc.cwl               | 2 +-
 cwl/gatk-haplotypecaller.cwl | 6 +++---
 cwl/samtools-index.cwl       | 2 +-
 cwl/samtools-sort.cwl        | 4 ++--
 5 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/cwl/bwa-gatk-wf.cwl b/cwl/bwa-gatk-wf.cwl
index 8069a1d..56c1758 100644
--- 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 4708aaf..888ba92 100644
--- 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 5480eac..ae34a00 100644
--- 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 3264f95..58ccbf7 100644
--- 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 8f1f273..cc7c23f 100644
--- 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
-- 
2.30.2