From 564d1400984f1925c77dae4b4bb43a42629f642f Mon Sep 17 00:00:00 2001
From: Danny Park <dpark@broadinstitute.org>
Date: Tue, 13 Dec 2022 08:35:53 -0500
Subject: [PATCH] add new workflow nextclade_single

---
 .dockstore.yml                           |  5 +++++
 pipes/WDL/workflows/nextclade_single.wdl | 20 ++++++++++++++++++++
 2 files changed, 25 insertions(+)
 create mode 100644 pipes/WDL/workflows/nextclade_single.wdl

diff --git a/.dockstore.yml b/.dockstore.yml
index 00d98dd64..7c238594c 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -244,6 +244,11 @@ workflows:
     primaryDescriptorPath: /pipes/WDL/workflows/multiqc_only.wdl
     testParameterFiles:
       - empty.json
+  - name: nextclade_single
+    subclass: WDL
+    primaryDescriptorPath: /pipes/WDL/workflows/nextclade_single.wdl
+    testParameterFiles:
+      - empty.json
   - name: sarscov2_batch_relineage
     subclass: WDL
     primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_batch_relineage.wdl
diff --git a/pipes/WDL/workflows/nextclade_single.wdl b/pipes/WDL/workflows/nextclade_single.wdl
new file mode 100644
index 000000000..59b57539b
--- /dev/null
+++ b/pipes/WDL/workflows/nextclade_single.wdl
@@ -0,0 +1,20 @@
+version 1.0
+
+import "../tasks/tasks_nextstrain.wdl" as nextstrain
+
+workflow nextclade_single {
+    meta {
+        description: "Run Nextclade on a single genome"
+    }
+
+    call nextstrain.nextclade_one_sample
+
+    output {
+        String nextclade_clade    = nextclade_one_sample.nextclade_clade
+        File   nextclade_tsv      = nextclade_one_sample.nextclade_tsv
+        File   nextclade_json     = nextclade_one_sample.nextclade_json
+        String nextclade_aa_subs  = nextclade_one_sample.aa_subs_csv
+        String nextclade_aa_dels  = nextclade_one_sample.aa_dels_csv
+        String nextclade_version  = nextclade_one_sample.nextclade_version
+    }
+}