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/awk-coverage.cwl | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 workflows/phylogeny/awk-coverage.cwl

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

diff --git a/workflows/phylogeny/awk-coverage.cwl b/workflows/phylogeny/awk-coverage.cwl
new file mode 100644
index 0000000..f7a357f
--- /dev/null
+++ b/workflows/phylogeny/awk-coverage.cwl
@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.1
+class: CommandLineTool
+
+baseCommand: awk
+
+inputs:
+  consensus_regex:
+    type: string
+    inputBinding:
+        position: 1
+
+  coverage_tsv:
+    type: File
+    inputBinding:
+        position: 2
+ 
+outputs:
+  awk_coverage_matrix:
+    type: stdout
+
+stdout: coverage.no_consensus.tsv
\ No newline at end of file
-- 
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