updating cwl

[arvados-tutorial.git] / cwl / samtools-index.cwl

diff --git a/cwl/samtools-index.cwl b/cwl/samtools-index.cwl
index 3264f95f62e8876f745899d95ddb95f0030a5e61..3876f3d2f233e80b19664a42b69c58bfd0eda2a5 100644 (file)
--- a/cwl/samtools-index.cwl
+++ b/cwl/samtools-index.cwl
@@ -1,6 +1,10 @@
 cwlVersion: v1.1
 class: CommandLineTool
 
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
 requirements:
   DockerRequirement:
     dockerPull: curii/bwa-samtools-picard
@@ -8,6 +12,10 @@ requirements:
     listing:
       - $(inputs.bam)
 
+hints:
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+
 inputs:
   bam: File
 
@@ -19,7 +27,7 @@ outputs:
     secondaryFiles:
       - .bai
 
-runcommand: samtools
+baseCommand: samtools
 
 arguments:
   - index