Simplify renaming logic for nextflu-private deploy

Simplifies the logic to rename Auspice JSONs for nextflu-private builds
to match what we were already doing manually and collects the "rename"
and "deploy" rules into a single Snakemake file.

Snakefile

@@ -37,10 +37,6 @@ include:  "workflow/snakemake_rules/fitness.smk"
 
 include:  "workflow/snakemake_rules/report.smk"
 
-if "custom_rules" in config:
-    for rule_file in config["custom_rules"]:
-        include: rule_file
-
 def _get_build_outputs():
     outputs = []
     for build_name, build_params in config["builds"].items():
@@ -60,6 +56,10 @@ def _get_build_outputs():
 
     return outputs
 
+if "custom_rules" in config:
+    for rule_file in config["custom_rules"]:
+        include: rule_file
+
 rule all:
     input:
         _get_build_outputs()

profiles/nextflu-private.yaml

@@ -2,7 +2,6 @@ custom_rules:
   - workflow/snakemake_rules/download_from_s3.smk
   - profiles/nextflu-private/antigenic_distances.smk
   - profiles/nextflu-private/report.smk
-  - profiles/nextflu-private/rename.smk
   - profiles/nextflu-private/deploy.smk
 
 # URL for auto-deploying builds
@@ -51,7 +50,6 @@ recency:
 
 builds:
   h1n1pdm_2y_titers:
-    auspice_name: "flu_seasonal_{build_date}_h1n1pdm_2y_titers_{segment}"
     lineage: h1n1pdm
     reference: "config/h1n1pdm/{segment}/reference.fasta"
     annotation: "config/h1n1pdm/{segment}/genemap.gff"
@@ -100,8 +98,6 @@ builds:
           # enabling titer models to be fit to egg-passaged data.
           filters: --query "(is_titer_strain == True)" --min-date {min_date} --exclude {exclude}
   h3n2_2y_titers:
-    # flu/seasonal/2023-10-26/h3n2/2y/titers/ha
-    auspice_name: "flu_seasonal_{build_date}_h3n2_2y_titers_{segment}"
     lineage: "h3n2"
     reference: "config/h3n2/{segment}/reference.fasta"
     annotation: "config/h3n2/{segment}/genemap.gff"
@@ -147,7 +143,6 @@ builds:
         title: "Cell-passaged HI titers from pooled human sera"
     subsamples: *titers-subsampling-scheme
   h3n2_2y:
-    auspice_name: "flu_seasonal_{build_date}_h3n2_2y_{segment}"
     lineage: "h3n2"
     reference: "config/h3n2/{segment}/reference.fasta"
     annotation: "config/h3n2/{segment}/genemap.gff"
@@ -185,7 +180,6 @@ builds:
       references:
           filters: --query "(is_reference == True)" --min-date {reference_min_date} --exclude {exclude}
   vic_2y_titers:
-    auspice_name: "flu_seasonal_{build_date}_vic_2y_titers_{segment}"
     lineage: vic
     reference: "config/vic/{segment}/reference.fasta"
     annotation: "config/vic/{segment}/genemap.gff"

profiles/nextflu-private/deploy.smk

@@ -1,14 +1,29 @@
 """
 This part of the workflow handles automatic deployments of nextflu-private builds.
-Depends on the `all_private` rule from rename.smk
 """
 
+rule all_private:
+    input:
+        jsons=_get_build_outputs(),
+    output:
+        json_dir=directory("auspice_renamed"),
+    params:
+        build_date=datetime.date.today().strftime("%Y-%m-%d"),
+    shell:
+        """
+        for file in {input.jsons}
+        do
+            ln ${{file}} {output.json_dir}/"flu_seasonal_{params.build_date}_`basename ${{file}}`"
+        done
+        """
+
 rule deploy_all:
-    input: rules.all_private.input
+    input:
+        json_dir=directory("auspice_renamed"),
     params:
         deploy_url = config["deploy_url"]
     shell:
         """
         nextstrain login --no-prompt;
-        nextstrain remote upload {params.deploy_url} {input}
+        nextstrain remote upload {params.deploy_url} {input.json_dir}/*.json
         """