From 9146f84f9bc0c8876818e84476debf23d7bb636f Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Wed, 12 Jun 2024 17:12:42 -0700 Subject: [PATCH] ingest: Include `seqName` in Nextclade output Resolves https://github.com/nextstrain/rsv/issues/65 Since Nextclade v3.7.0, the `seqName` column needs to be explicitly listed when using the `--output-columns-selection` option. --- ingest/workflow/snakemake_rules/sort.smk | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/ingest/workflow/snakemake_rules/sort.smk b/ingest/workflow/snakemake_rules/sort.smk index ea8e79c..fda5046 100644 --- 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} """ -