Merge branch 'dev' into patch-modules

Author: Joon-Klaps

CHANGELOG.md

@@ -30,6 +30,7 @@ Initial release of Joon-Klaps/viralgenie, created with the [nf-core](https://nf-
 - fixing null output from global prefix ([#147](https://github.com/Joon-Klaps/viralgenie/pull/147))
 - Fix empty filtered clusters ([#148](https://github.com/Joon-Klaps/viralgenie/pull/148))
 - Fixing missing columns from general stats & add general stats sample filtering ([#149](https://github.com/Joon-Klaps/viralgenie/pull/149))
+- process.shell template fix ([#157](https://github.com/Joon-Klaps/viralgenie/pull/157)) - see also [nf-core/tools #3416](https://github.com/nf-core/tools/pull/3416)
 
 ### `Parameters`
 - New parameter mmseqs_cluster_mode default to 0 ([#130](https://github.com/Joon-Klaps/viralgenie/pull/130))

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