updating cwl

[arvados-tutorial.git] / cwl / bwamem-samtools-view.cwl

diff --git a/cwl/bwamem-samtools-view.cwl b/cwl/bwamem-samtools-view.cwl
index 044ef74e524732397d06b052087ea288c59a33c7..efc423e27db676afea44d840a826cff7e7584c51 100644 (file)
--- a/cwl/bwamem-samtools-view.cwl
+++ b/cwl/bwamem-samtools-view.cwl
@@ -1,6 +1,9 @@
 cwlVersion: v1.1
 class: CommandLineTool
 label: Realigning fastqs and converting output to bam
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
 
 requirements:
   DockerRequirement:
@@ -8,7 +11,11 @@ requirements:
   ShellCommandRequirement: {}
   ResourceRequirement:
     ramMin: 26000
-    coresMin: 8
+    coresMin: 16 
+
+hints:
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
 
 inputs:
   reference:
@@ -36,17 +43,22 @@ outputs:
 arguments:
   - /bwa-0.7.17/bwa
   - mem
+  - -M
   - -t
   - $(runtime.cores)
   - $(inputs.reference)
   - -R
-  - "@RG\\tID:sample\\tSM:sample\\tLB:sample\\tPL:ILLUMINA"
+  - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1' 
+  - -c
+  - 250
   - $(inputs.fastq1)
   - $(inputs.fastq2)
   - shellQuote: false
     valueFrom: '|'
   - samtools
   - view
+  - -@
+  - $(runtime.cores)
   - -b
   - -S
   - shellQuote: false