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Add no clobber and put bash options on their own line #2991

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Merged
merged 2 commits into from
May 22, 2024
Merged

Add no clobber and put bash options on their own line #2991

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Add no clobber and put bash options on their own line
mahesh-panchal May 21, 2024
589265e
[automated] Update CHANGELOG.md
nf-core-bot May 21, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -17,6 +17,7 @@
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974))
- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982))
- Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
- Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991))

## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]

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11 changes: 9 additions & 2 deletions nf_core/pipeline-template/nextflow.config
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Expand Up @@ -220,8 +220,15 @@ env {
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// 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.
"""

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
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