Set final targets

Set final targets to be the pair of metadata_denvX.tsv and sequences_denvX.fasta files.
nextstrain · Dec 6, 2023 · e638db2 · e638db2
1 parent bd9b420
commit e638db2
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Showing 3 changed files with 15 additions and 3 deletions.
diff --git a/ingest/Snakefile b/ingest/Snakefile
@@ -11,10 +11,11 @@ if not config:
 
 send_slack_notifications = config.get("send_slack_notifications", False)
 
+serotypes = ['all', 'denv1', 'denv2', 'denv3', 'denv4']
 
 def _get_all_targets(wildcards):
     # Default targets are the metadata TSV and sequences FASTA files
-    all_targets = ["results/sequences.fasta", "results/metadata.tsv"]
+    all_targets = expand(["results/sequences_{serotype}.fasta", "results/metadata_{serotype}.tsv"], serotype=serotypes)
 
     # Add additional targets based on upload config
     upload_config = config.get("upload", {})

diff --git a/ingest/config/optional.yaml b/ingest/config/optional.yaml
@@ -10,8 +10,16 @@ upload:
     files_to_upload:
       genbank.ndjson.xz: data/genbank.ndjson
       all_sequences.ndjson.xz: data/sequences.ndjson
-      metadata.tsv.gz: results/metadata.tsv
-      sequences.fasta.xz: results/sequences.fasta
+      metadata_all.tsv.zst: results/metadata_all.tsv
+      sequences_all.fasta.zst: results/sequences_all.fasta
+      metadata_denv1.tsv.zst: results/metadata_denv1.tsv
+      sequences_denv1.fasta.zst: results/sequences_denv1.fasta
+      metadata_denv2.tsv.zst: results/metadata_denv2.tsv
+      sequences_denv2.fasta.zst: results/sequences_denv2.fasta
+      metadata_denv3.tsv.zst: results/metadata_denv3.tsv
+      sequences_denv3.fasta.zst: results/sequences_denv3.fasta
+      metadata_denv4.tsv.zst: results/metadata_denv4.tsv
+      sequences_denv4.fasta.zst: results/sequences_denv4.fasta
       alignment.fasta.xz: data/alignment.fasta
       insertions.csv.gz: data/insertions.csv
       translations.zip: data/translations.zip

diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
@@ -29,12 +29,15 @@ rule split_dengue_sequences:
         metadata="results/metadata.tsv",
         nextclade_all_results="results/nextclade_results/nextclade_all.tsv",
     output:
+        sequences_all="results/sequences_all.fasta",
         sequences_denv1="results/sequences_denv1.fasta",
         sequences_denv2="results/sequences_denv2.fasta",
         sequences_denv3="results/sequences_denv3.fasta",
         sequences_denv4="results/sequences_denv4.fasta",
     shell:
         """
+        cp {input.sequences} {output.sequences_all}
+        
         augur filter \
           --sequences {input.sequences} \
           --metadata {input.nextclade_all_results} \