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authorNjagi Mwaniki2021-01-26 13:44:01 +0300
committerNjagi Mwaniki2021-01-26 15:06:57 +0300
commit4842117f530aba08b4a253aee533a8d4802b1c12 (patch)
tree150bef4a574486db9e7c16d87be89ad219d84bb1 /workflows/phylogeny/coverage.cwl
parentb112b3203e34ea61dfdf802bce5036f938eaa774 (diff)
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Add phylogeny workflow
Signed-off-by: Njagi Mwaniki <njagi@urbanslug.com>
Diffstat (limited to 'workflows/phylogeny/coverage.cwl')
-rw-r--r--workflows/phylogeny/coverage.cwl36
1 files changed, 36 insertions, 0 deletions
diff --git a/workflows/phylogeny/coverage.cwl b/workflows/phylogeny/coverage.cwl
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index 0000000..ed706ca
--- /dev/null
+++ b/workflows/phylogeny/coverage.cwl
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+#!/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