Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>

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

diff --git a/cwl/samtools-index.cwl b/cwl/samtools-index.cwl
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+cwlVersion: v1.1
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: curii/bwa-samtools-picard
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.bam)
+
+arguments:
+  - samtools
+  - index
+  - $(inputs.bam.basename)
+
+inputs:
+  bam: File
+
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: "*bam"
+    secondaryFiles:
+      - .bai
+