From 29f17c977d10588a601a7c4bd46d1b0ebb7de208 Mon Sep 17 00:00:00 2001 From: Alex Thomas Date: Thu, 22 Feb 2024 10:52:50 +0000 Subject: [PATCH] fix pipe of stderr --- workflow/rules/ref.smk | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk index fa19e65b..6c0131c8 100644 --- 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: