Merge pull request #444 from broadinstitute/dp-nextclade

add new workflow nextclade_single
broadinstitute · Dec 13, 2022 · e0b1f76 · e0b1f76
2 parents d4c3ff0 + 564d140
commit e0b1f76
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diff --git 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
@@ -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
+    }
+}