Ingest: Remove Nextclade

If pathogen is not listed in nextclade_data, remove nextclade rules and scripts until it is added. https://github.com/nextstrain/nextclade_data/tree/release/data/datasets
nextstrain · Apr 17, 2023 · 901148e · 901148e
1 parent a7c7a4c
commit 901148e
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Showing 3 changed files with 1 addition and 70 deletions.
diff --git a/ingest/Snakefile b/ingest/Snakefile
@@ -64,7 +64,6 @@ rule all:
 
 include: "workflow/snakemake_rules/fetch_sequences.smk"
 include: "workflow/snakemake_rules/transform.smk"
-include: "workflow/snakemake_rules/nextclade.smk"
 
 
 if config.get("upload"):

diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
diff --git a/ingest/workflow/snakemake_rules/transform.smk b/ingest/workflow/snakemake_rules/transform.smk
@@ -41,7 +41,7 @@ rule transform:
         sequences_ndjson="data/sequences.ndjson",
         all_geolocation_rules="data/all-geolocation-rules.tsv",
     output:
-        metadata="data/metadata_raw.tsv",
+        metadata="data/metadata.tsv",
         sequences="data/sequences.fasta",
     log:
         "logs/transform.txt",