updating cwl

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

diff --git a/cwl/samtools-sort.cwl b/cwl/samtools-sort.cwl
index cc7c23f0535b4c0124652ea36712779cf84da702..c94d681a99aa5b73ef7b29142c99c47ec19746e7 100644 (file)
--- a/cwl/samtools-sort.cwl
+++ b/cwl/samtools-sort.cwl
@@ -1,14 +1,26 @@
 cwlVersion: v1.1
 class: CommandLineTool
 
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
 requirements:
   DockerRequirement:
     dockerPull: curii/bwa-samtools-picard
   ShellCommandRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.bam)
   ResourceRequirement:
-    ramMin: 10000
+    ramMin: 20000
     coresMin: 4
 
+hints:
+  arv:RuntimeConstraints:
+    keep_cache: 9216 
+    outputDirType: keep_output_dir
+
 inputs:
   bam: File
   sample: string
@@ -23,8 +35,10 @@ baseCommand: samtools
 
 arguments:
   - sort
-  - -t
+  - -@
   - $(runtime.cores)
-  - $(inputs.bam)
+  - $(inputs.bam.basename)
+  - -m
+  - '2G'
   - -o
-  - $(runtime.outdir)/$(inputs.sample).sorted.bam
+  - $(inputs.sample).sorted.bam