fixup replace: parameterize the nextclade key fields

nextstrain · Oct 10, 2023 · 1a68589 · 1a68589
1 parent 89c89c7
commit 1a68589
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/ingest/config/config.yaml b/ingest/config/config.yaml
@@ -44,6 +44,8 @@ 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

diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
@@ -61,6 +61,7 @@ rule join_metadata_clades:
         metadata="data/metadata.tsv",
     params:
         id_field=config["transform"]["id_field"],
+        nextclade_id_field=config["transform"]["nextclade_id_field"],
     shell:
         """
         export SUBSET_FIELDS=`awk 'NR>1 {{print $1}}' {input.nextclade_field_map} | tr '\n' ',' | sed 's/,$//g'`
@@ -75,11 +76,11 @@ rule join_metadata_clades:
             -k {input.nextclade_field_map} \
         | tsv-join -H \
             --filter-file - \
-            --key-fields seqName \
+            --key-fields {params.nextclade_id_field} \
             --data-fields {params.id_field} \
             --append-fields '*' \
             --write-all ? \
             {input.metadata} \
-        | tsv-select -H --exclude seqName \
+        | tsv-select -H --exclude {params.nextclade_id_field} \
             > {output.metadata}
         """