From d1f6dc7f2d348be313e867066448e2720b02c19a Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 21 Jan 2025 14:43:13 +0100 Subject: [PATCH] Fix 'process.shell' in nextflow.config --- nf_core/pipeline-template/nextflow.config | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 5bbe47d9d..217b1c254 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -238,14 +238,13 @@ env { } // Set bash options -process.shell = """\ -bash - -set -e # Exit if a tool returns a non-zero status/exit code -set -u # Treat unset variables and parameters as an error -set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute -set -C # No clobber - prevent output redirection from overwriting files. -""" +process.shell = [ + "bash", + "-C", // No clobber - prevent output redirection from overwriting files. + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false