updating cwl

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

diff --git a/cwl/old/samtools-sort.cwl b/cwl/old/samtools-sort.cwl
new file mode 100644 (file)
index 0000000..cc7c23f
--- /dev/null
+++ b/cwl/old/samtools-sort.cwl
@@ -0,0 +1,30 @@
+cwlVersion: v1.1
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: curii/bwa-samtools-picard
+  ShellCommandRequirement: {}
+  ResourceRequirement:
+    ramMin: 10000
+    coresMin: 4
+
+inputs:
+  bam: File
+  sample: string
+
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: "*sorted.bam"
+
+baseCommand: samtools
+
+arguments:
+  - sort
+  - -t
+  - $(runtime.cores)
+  - $(inputs.bam)
+  - -o
+  - $(runtime.outdir)/$(inputs.sample).sorted.bam