Remove Nextclade related rules

Removal of Nextclade related rules, pending the compilation of a Nextclade zika dataset and potential v3 changes.
nextstrain · Nov 13, 2023 · c475361 · c475361
1 parent 38007bb
commit c475361
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Showing 5 changed files with 2 additions and 111 deletions.
diff --git a/ingest/Snakefile b/ingest/Snakefile
@@ -57,7 +57,6 @@ 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", False):

diff --git a/ingest/config/config.yaml b/ingest/config/config.yaml
@@ -71,9 +71,3 @@ transform:
     'institution'
   ]
 
-# Params for Nextclade related rules
-nextclade:
-  # Field to use as the sequence ID in the Nextclade file
-  id_field: 'seqName'
-  # Fields from a Nextclade file to be renamed (if desired) and appended to a metadata file
-  field_map: 'source-data/nextclade-field-map.tsv'
diff --git a/ingest/source-data/nextclade-field-map.tsv b/ingest/source-data/nextclade-field-map.tsv
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
@@ -6,7 +6,7 @@ formats and expects input file
 
 This will produce output files as
 
-    metadata = "data/metadata_raw.tsv"
+    metadata = "results/metadata.tsv"
     sequences = "results/sequences.fasta"
 
 Parameters are expected to be defined in `config.transform`.
@@ -42,7 +42,7 @@ rule transform:
         all_geolocation_rules="data/all-geolocation-rules.tsv",
         annotations=config["transform"]["annotations"],
     output:
-        metadata="data/metadata_raw.tsv",
+        metadata="results/metadata.tsv",
         sequences="results/sequences.fasta",
     log:
         "logs/transform.txt",