X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/cc2f0d302b6f536f680a8459b12ec9972c9507ff:/cwl/helper/samtools-fixmate.cwl..80edc41f30dcc8a04f9462b9a7f58ae737f96267:/cwl/helper/not-in-use/static/gitweb.css

diff --git a/cwl/helper/samtools-fixmate.cwl b/cwl/helper/samtools-fixmate.cwl
deleted file mode 100644
index 61d5c1f..0000000
--- a/cwl/helper/samtools-fixmate.cwl
+++ /dev/null
@@ -1,37 +0,0 @@
-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