fixup replace: use a nextclade config section

nextstrain · Oct 11, 2023 · 9817e6e · 9817e6e
1 parent 5b879a1
commit 9817e6e
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/ingest/config/config.yaml b/ingest/config/config.yaml
@@ -44,8 +44,6 @@ transform:
   annotations: 'source-data/annotations.tsv'
   # ID field used to merge annotations
   annotations_id: 'accession'
-  # Field to use as the sequence ID in the Nextclade file
-  nextclade_id_field: 'seqName'
   # Field to use as the sequence ID in the FASTA file
   id_field: 'accession'
   # Field to use as the sequence in the FASTA file
@@ -68,3 +66,10 @@ transform:
     'authors',
     '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/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
@@ -56,12 +56,12 @@ rule join_metadata_clades:
     input:
         nextclade="data/nextclade.tsv",
         metadata="data/metadata_raw.tsv",
-        nextclade_field_map="source-data/nextclade-field-map.tsv",
+        nextclade_field_map=config["nextclade"]["field_map"],
     output:
         metadata="data/metadata.tsv",
     params:
         id_field=config["transform"]["id_field"],
-        nextclade_id_field=config["transform"]["nextclade_id_field"],
+        nextclade_id_field=config["nextclade"]["id_field"],
     shell:
         """
         export SUBSET_FIELDS=`awk 'NR>1 {{print $1}}' {input.nextclade_field_map} | tr '\n' ',' | sed 's/,$//g'`