ingest: Include seqName in Nextclade output

Resolves #65 Since Nextclade v3.7.0, the `seqName` column needs to be explicitly listed when using the `--output-columns-selection` option.
nextstrain · Jun 13, 2024 · 9146f84 · 9146f84
1 parent c3b634b
commit 9146f84
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/ingest/workflow/snakemake_rules/sort.smk b/ingest/workflow/snakemake_rules/sort.smk
@@ -60,7 +60,7 @@ rule nextclade:
         nextclade = "data/{type}/nextclade.tsv"
     params:
         dataset = "rsv-{type}_nextclade",
-        output_columns = "clade qc.overallScore qc.overallStatus alignmentScore  alignmentStart  alignmentEnd  coverage dynamic"
+        output_columns = "seqName clade qc.overallScore qc.overallStatus alignmentScore  alignmentStart  alignmentEnd  coverage dynamic"
     threads: 8
     shell:
         """
@@ -84,4 +84,3 @@ rule extend_metadata:
                                        --nextclade {input.nextclade} \
                                        --output {output.metadata}
         """
-