diff --git a/ingest/workflow/snakemake_rules/sort.smk b/ingest/workflow/snakemake_rules/sort.smk index d5d6d4f..ea8e79c 100644 --- a/ingest/workflow/snakemake_rules/sort.smk +++ b/ingest/workflow/snakemake_rules/sort.smk @@ -61,9 +61,10 @@ rule nextclade: params: dataset = "rsv-{type}_nextclade", output_columns = "clade qc.overallScore qc.overallStatus alignmentScore alignmentStart alignmentEnd coverage dynamic" + threads: 8 shell: """ - nextclade3 run -D {params.dataset} \ + nextclade3 run -D {params.dataset} -j {threads} \ --output-columns-selection {params.output_columns} \ --output-tsv {output.nextclade} \ {input.sequences}