From b7589c057cfbd60c8ab74aa808fb7a37afd4a445 Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Wed, 10 Jul 2024 09:33:54 -0700
Subject: [PATCH] Pass threads to Nextclade

Follow up to https://github.com/nextstrain/ncov-ingest/pull/460
---
 workflow/snakemake_rules/nextclade.smk | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/workflow/snakemake_rules/nextclade.smk b/workflow/snakemake_rules/nextclade.smk
index e97c8aaf..5e71e310 100644
--- a/workflow/snakemake_rules/nextclade.smk
+++ b/workflow/snakemake_rules/nextclade.smk
@@ -208,6 +208,7 @@ rule run_wuhan_nextclade:
         fi
 
         ./{input.nextclade_path} run \
+        -j {threads} \
         {input.sequences}\
         --input-dataset={input.dataset} \
         --output-tsv={output.info} \
@@ -239,6 +240,7 @@ rule run_21L_nextclade:
         fi
 
         ./{input.nextclade_path} run \
+        -j {threads} \
         {input.sequences} \
         --input-dataset={input.dataset} \
         --output-tsv={output.info} \