From c40fcb7398d6e5e73e99092f5db383a0c32119b4 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 14:26:13 +0000 Subject: [PATCH] manually add template fix with latest nextflow version --- nextflow.config | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/nextflow.config b/nextflow.config index f004ec97..a7f72aae 100644 --- a/nextflow.config +++ b/nextflow.config @@ -252,14 +252,13 @@ 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