Add phylogeny workflow

Signed-off-by: Njagi Mwaniki <njagi@urbanslug.com>

1 files changed, 49 insertions, 0 deletions

diff --git a/workflows/phylogeny/newick.cwl b/workflows/phylogeny/newick.cwl
new file mode 100644
index 0000000..e1e78f7
--- /dev/null
+++ b/workflows/phylogeny/newick.cwl
@@ -0,0 +1,49 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.1
+
+class: CommandLineTool
+baseCommand: python
+
+inputs:
+    main_py_script:
+        type: File
+        inputBinding:
+            position: 1
+
+    newick:
+        type: string
+        inputBinding:
+            position: 2
+
+    newick_dimensions:
+        type: int
+        inputBinding:
+            position: 3
+            prefix: -d
+
+    newick_coverage_matrix:
+        type: File
+        inputBinding:
+            position: 3
+    
+    newick_metadata:
+        type: string
+        inputBinding:
+            position: 4
+
+    newick_tree:
+        type: string
+        inputBinding:
+            position: 5
+
+outputs:
+    metadata_out:
+        type: File
+        outputBinding:
+            glob: 'metadata.tsv'
+
+    newick_tree_out:
+        type: File
+        outputBinding:
+            glob: '*.nwk'
\ No newline at end of file