From 535b8017ddd27a9db683f6d29368258b5c48cf5a Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Fri, 3 Jul 2020 20:45:17 +0000
Subject: Improving genbank import workflow

---
 scripts/import_from_genbank.cwl | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 scripts/import_from_genbank.cwl

(limited to 'scripts/import_from_genbank.cwl')

diff --git a/scripts/import_from_genbank.cwl b/scripts/import_from_genbank.cwl
new file mode 100644
index 0000000..dcf9acb
--- /dev/null
+++ b/scripts/import_from_genbank.cwl
@@ -0,0 +1,27 @@
+cwlVersion: v1.1
+class: Workflow
+inputs:
+  existing_metadata_from_nuccore:
+    type: Directory?
+outputs: []
+requirements:
+  ScatterFeatureRequirement: {}
+steps:
+  fetch_from_genbank:
+    in:
+      existing_metadata_from_nuccore: existing_metadata_from_nuccore
+    out: [fasta_and_yaml, metadata_from_nuccore, accessions]
+    run: fetch_from_genbank.cwl
+  split_into_arrays:
+    in:
+      dir: fetch_from_genbank/fasta_and_yaml
+    out: [fasta, metadata]
+    run: split_into_arrays.cwl
+  upload:
+    in:
+      fasta: split_into_arrays/fasta
+      metadata: split_into_arrays/metadata
+    out: []
+    scatter: [fasta, metadata]
+    scatterMethod: dotproduct
+    run: upload.cwl
-- 
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