Rearranging for clarity

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

diff --git a/cwl/helper/samtools-index.cwl b/cwl/helper/samtools-index.cwl
deleted file mode 100644 (file)
index d479fbd..0000000
--- a/cwl/helper/samtools-index.cwl
+++ /dev/null
@@ -1,35 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-label: Indexing Bam File
-
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
-
-requirements:
-  DockerRequirement:
-    dockerPull: curii/bwa-samtools-picard
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
-
-hints:
-  arv:RuntimeConstraints:
-    outputDirType: keep_output_dir
-
-inputs:
-  bam: File
-
-outputs:
-  indexedbam:
-    type: File
-    outputBinding:
-      glob: "*bam"
-    secondaryFiles:
-      - .bai
-
-baseCommand: samtools
-
-arguments:
-  - index
-  - $(inputs.bam.basename)