fix pipe of stderr

IKIM-Essen · Feb 22, 2024 · 29f17c9 · 29f17c9
1 parent c6fc415
commit 29f17c9
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
@@ -163,7 +163,7 @@ rule get_genome_db_for_kraken:
     conda:
         "../envs/unix.yaml"
     shell:
-        "mkdir {output} && curl -SL https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20220926.tar.gz | tar zxvf - -C {output} 2> {log}"
+        "(mkdir {output} && curl -SL https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20220926.tar.gz | tar zxvf - -C {output}) 2> {log}"
 
 
 rule get_taxonomie_db_for_krona:
@@ -221,7 +221,7 @@ rule update_lineages:
 
 rule get_gisaid_provision:
     output:
-        temp("resources/gisaid/provision.json"),
+        "resources/gisaid/provision.json",
     log:
         "logs/get_gisaid_provision.log",
     conda: