From d2708b7b6591678c46b1a1bf026d143744c46319 Mon Sep 17 00:00:00 2001 From: Chris Tomkins-Tinch Date: Tue, 24 Nov 2020 21:38:52 -0500 Subject: [PATCH] set "-o pipefail" for filter_subsample_sequences and mafft_one_chr Previously, if the commands along the way in the pipeline fail, the tasks succeed. This adds "-o pipefail" so errors lead to non-zero exits. This change may be needed elsewhere; only adding to these two tasks for now. --- pipes/WDL/tasks/tasks_nextstrain.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 023b5236b..2fdcb5fdf 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -128,7 +128,7 @@ task filter_subsample_sequences { } String out_fname = sub(sub(basename(sequences_fasta), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta") command { - set -e + set -e -o pipefail augur version > VERSION touch wherefile @@ -265,7 +265,7 @@ task mafft_one_chr { Int cpus = 32 } command { - set -e + set -e -o pipefail touch args.txt # boolean options