From c5553ef7b517655f7d01fa5f7f6fb873f79d4004 Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Tue, 20 Feb 2024 16:26:14 +0100
Subject: [PATCH] Don't error if nextclade input sequences empty, necessary
 because of  https://github.com/nextstrain/nextclade/issues/1422

---
 workflow/snakemake_rules/nextclade.smk | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/workflow/snakemake_rules/nextclade.smk b/workflow/snakemake_rules/nextclade.smk
index 3d0bc127..c31077c0 100644
--- a/workflow/snakemake_rules/nextclade.smk
+++ b/workflow/snakemake_rules/nextclade.smk
@@ -187,6 +187,14 @@ rule run_wuhan_nextclade:
         ],
     shell:
         """
+        # If there are no sequences to run Nextclade on, create empty output files
+        if [[ ! -s {input.sequences} ]]; then
+            touch {output.info}
+            touch {output.alignment}
+            touch {output.translations}
+            exit 0
+        fi
+
         ./{input.nextclade_path} run \
         {input.sequences}\
         --input-dataset={input.dataset} \
@@ -208,6 +216,12 @@ rule run_21L_nextclade:
         info=f"data/{database}/nextclade_21L_new_raw.tsv",
     shell:
         """
+        # If there are no sequences to run Nextclade on, create empty output files
+        if [[ ! -s {input.sequences} ]]; then
+            touch {output.info}
+            exit 0
+        fi
+
         ./{input.nextclade_path} run \
         {input.sequences} \
         --input-dataset={input.dataset} \