Merge pull request #124 from urbanslug/master

Add phylogeny workflow

1 files changed, 61 insertions, 0 deletions

diff --git a/workflows/phylogeny/align.cwl b/workflows/phylogeny/align.cwl
new file mode 100644
index 0000000..cb2484e
--- /dev/null
+++ b/workflows/phylogeny/align.cwl
@@ -0,0 +1,61 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.1
+
+class: CommandLineTool
+baseCommand: pggb
+
+inputs:
+  threads:
+    type: int
+    inputBinding:
+        position: 1
+        prefix: -t
+
+  pggb_wfmash:
+    type: boolean
+    inputBinding:
+        position: 2
+        prefix: --wfmash
+
+  pggb_fasta:
+    type: File
+    inputBinding:
+        position: 3
+        prefix: -i
+
+  pggb_mash_k_mer:
+    type: int
+    inputBinding:
+        position: 4
+        prefix: -K
+
+  pggb_map_percent_identity:
+    type: int
+    inputBinding:
+        position: 5
+        prefix: -p
+
+  pggb_num_secondary_mappings:
+    type: int
+    inputBinding:
+        position: 6
+        prefix: -n
+
+  pggb_segment_length:
+    type: int
+    inputBinding:
+        position: 7
+        prefix: -s
+
+  pggb_output_dir:
+    type: string
+    inputBinding:
+        position: 8
+        prefix: -o
+
+outputs:
+    pggb_odgi_graph:
+        type: File
+        outputBinding:
+            glob: '*.smooth.og'
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