From d781e42c9adac07253cb928ae66e9b7314710267 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 20 Apr 2020 12:55:18 -0400
Subject: Move workflows into main repo

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 workflows/pangenome-generate/odgi_to_rdf.cwl | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 workflows/pangenome-generate/odgi_to_rdf.cwl

(limited to 'workflows/pangenome-generate/odgi_to_rdf.cwl')

diff --git a/workflows/pangenome-generate/odgi_to_rdf.cwl b/workflows/pangenome-generate/odgi_to_rdf.cwl
new file mode 100644
index 0000000..079d6fb
--- /dev/null
+++ b/workflows/pangenome-generate/odgi_to_rdf.cwl
@@ -0,0 +1,25 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+  DockerRequirement:
+    dockerPull: spodgi/spodgi
+requirements:
+  InlineJavascriptRequirement: {}
+  ShellCommandRequirement: {}
+inputs:
+  - id: odgi
+    type: File
+  - id: output_name
+    type: string?
+
+stdout: $(inputs.output_name || inputs.odgi.nameroot+'.ttl.xz')
+
+arguments:
+  [odgi_to_rdf.py, $(inputs.odgi), "-",
+   {valueFrom: "|", shellQuote: false},
+   xz, --stdout]
+
+outputs:
+  - id: rdf
+    type: stdout
-- 
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