updating cwl

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

diff --git a/cwl/samtools-fixmate.cwl b/cwl/samtools-fixmate.cwl
new file mode 100644 (file)
index 0000000..61d5c1f
--- /dev/null
+++ b/cwl/samtools-fixmate.cwl
@@ -0,0 +1,37 @@
+cwlVersion: v1.1
+class: CommandLineTool
+
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  DockerRequirement:
+    dockerPull: curii/bwa-samtools-picard
+  ShellCommandRequirement: {}
+  ResourceRequirement:
+    ramMin: 10000
+    coresMin: 4
+
+hints:
+  arv:RuntimeConstraints:
+    outputDirType: keep_output_dir
+
+inputs:
+  bam: File
+  sample: string
+
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: "*fixed.bam"
+
+baseCommand: samtools
+
+arguments:
+  - fixmate 
+  - -O
+  - "bam"
+  - $(inputs.bam.path)
+  - $(runtime.outdir)/$(inputs.sample).fixed.bam