From 4842117f530aba08b4a253aee533a8d4802b1c12 Mon Sep 17 00:00:00 2001
From: Njagi Mwaniki
Date: Tue, 26 Jan 2021 13:44:01 +0300
Subject: Add phylogeny workflow

Signed-off-by: Njagi Mwaniki <njagi@urbanslug.com>
---
 workflows/phylogeny/coverage.cwl | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 workflows/phylogeny/coverage.cwl

(limited to 'workflows/phylogeny/coverage.cwl')

diff --git a/workflows/phylogeny/coverage.cwl b/workflows/phylogeny/coverage.cwl
new file mode 100644
index 0000000..ed706ca
--- /dev/null
+++ b/workflows/phylogeny/coverage.cwl
@@ -0,0 +1,36 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.1
+
+class: CommandLineTool
+baseCommand: odgi
+
+inputs:
+  odgi_paths:
+    type: string
+    inputBinding:
+      position: 1
+
+  odgi_graph:
+    type: File
+    inputBinding:
+        position: 2
+        prefix: -i
+
+  haplotypes:
+    type: boolean
+    inputBinding:
+      position: 4
+      prefix: -H
+
+  threads:
+    type: int
+    inputBinding:
+        position: 5
+        prefix: -t
+
+outputs:
+  coverage_matrix:
+    type: stdout
+
+stdout: coverage.tsv
\ No newline at end of file
-- 
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