From bef69f2313ec3fb619e4850e3bccfb86d11d9087 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 21 Jan 2025 15:12:22 +0000 Subject: [PATCH 1/2] Add newlines and set command to fix #3416 --- nf_core/pipeline-template/nextflow.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 217b1c254..de6e0fac9 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -240,10 +240,10 @@ env { // Set bash options 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 + "\nset -C", // No clobber - prevent output redirection from overwriting files. + "\nset -e", // Exit if a tool returns a non-zero status/exit code + "\nset -u", // Treat unset variables and parameters as an error + "\nset -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. From a76afa35865ec3e8c0ee32d9c9a6055e24517f7d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 21 Jan 2025 15:14:41 +0000 Subject: [PATCH 2/2] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ecb4fcb93..1ad7b11c0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ ### General - Fix `process.shell` in `nextflow.config` ([#3416](https://github.com/nf-core/tools/pull/3416)) +- Add newlines and set command to fix #3416 ([#3417](https://github.com/nf-core/tools/pull/3417)) ## [v3.1.2 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.2) - [2025-01-20]