diff --git a/nextflow.config b/nextflow.config index 782edeb5..2e5463d7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -344,14 +344,14 @@ 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