1 files changed, 36 insertions, 0 deletions
diff --git a/workflows/phylogeny/augur.cwl b/workflows/phylogeny/augur.cwl
new file mode 100644
index 0000000..4676333
--- /dev/null
+++ b/workflows/phylogeny/augur.cwl
@@ -0,0 +1,36 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.1
+
+class: CommandLineTool
+baseCommand: bash
+
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.dataDir)
+
+inputs:
+    nextstrain_bash_script:
+        type: File
+        inputBinding:
+            position: 1
+
+    newick_tree_2:
+        type: File
+        inputBinding:
+            position: 2
+
+    metadata_newick:
+        type: File
+        inputBinding:
+            position: 3
+
+    dataDir:
+        type: Directory
+
+outputs:
+    newick_json:
+        type: File
+        outputBinding:
+            glob: 'covid.json'
+\ No newline at end of file