Merge pull request #3416 from ewels/fix-process-shell

Template: Fix `process.shell` in `nextflow.config`
nf-core · Jan 21, 2025 · 0b6b151 · 0b6b151
2 parents 0716d91 + 702e00c
commit 0b6b151
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,8 @@
 
 ### General
 
+- Fix `process.shell` in `nextflow.config` ([#3416](https://github.com/nf-core/tools/pull/3416))
+
 ## [v3.1.2 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.2) - [2025-01-20]
 
 ### Template

diff --git 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