Add phylo automation config

phylogenetic/Snakefile

@@ -2,8 +2,8 @@ configfile: "defaults/config.yaml"
 
 rule all:
     input:
-        auspice_json=expand("auspice/yellow-fever-virus_{build}.json", build=config["builds"]),
-        tip_frequencies_json=expand("auspice/yellow-fever-virus_{build}_tip-frequencies.json", build=config["builds"]),
+        auspice_json=expand("auspice/yellow-fever_{build}.json", build=config["builds"]),
+        tip_frequencies_json=expand("auspice/yellow-fever_{build}_tip-frequencies.json", build=config["builds"]),
 
 
 include: "rules/prepare_sequences.smk"

phylogenetic/build-configs/nextstrain-automation/config.yaml

@@ -0,0 +1,4 @@
+custom_rules:
+  - build-configs/nextstrain-automation/deploy.smk
+
+deploy_url: "s3://nextstrain-data"

phylogenetic/build-configs/nextstrain-automation/deploy.smk

@@ -0,0 +1,15 @@
+"""
+This part of the workflow handles automatic deployments of the measles build.
+Uploads the build defined as the default output of the workflow through
+the `all` rule from Snakefille
+"""
+
+rule deploy_all:
+    input: *rules.all.input
+    output: touch("results/deploy_all.done")
+    params:
+        deploy_url = config["deploy_url"]
+    shell:
+        """
+        nextstrain remote upload {params.deploy_url} {input}
+        """

phylogenetic/rules/export.smk

@@ -33,7 +33,7 @@ rule export:
         auspice_config = lambda w: config["files"][w.build]["auspice_config"],
         description=config["files"]["description"],
     output:
-        auspice_json = "auspice/yellow-fever-virus_{build}.json"
+        auspice_json = "auspice/yellow-fever_{build}.json"
     params:
         metadata_columns = config["export"]["metadata_columns"],
         strain_id = config["strain_id_field"],
@@ -66,7 +66,7 @@ rule tip_frequencies:
         tree = "results/{build}/tree.nwk",
         metadata = "data/metadata.tsv"
     output:
-        tip_freq = "auspice/yellow-fever-virus_{build}_tip-frequencies.json"
+        tip_freq = "auspice/yellow-fever_{build}_tip-frequencies.json"
     params:
         strain_id = config["strain_id_field"],
         min_date = config["tip_frequencies"]["min_date"],