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-o pipefail newline #3425

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Merged
merged 2 commits into from
Jan 27, 2025
Merged

-o pipefail newline #3425

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f8b099c
Separate -o pipefail into separate list elements
ewels Jan 27, 2025
2d7e1a6
[automated] Update CHANGELOG.md
nf-core-bot Jan 27, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -20,6 +20,7 @@

- Fix `process.shell` in `nextflow.config` ([#3416](https://github.com/nf-core/tools/pull/3416))
- Update python:3.12-slim Docker digest to 123be56 ([#3421](https://github.com/nf-core/tools/pull/3421))
- `-o pipefail` newline ([#3425](https://github.com/nf-core/tools/pull/3425))

## [v3.1.2 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.2) - [2025-01-20]

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3 changes: 2 additions & 1 deletion nf_core/pipeline-template/nextflow.config
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Expand Up @@ -243,7 +243,8 @@ process.shell = [
"-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
"-o", // Returns the status of the last command to exit..
"pipefail" // ..with a non-zero status or zero if all successfully execute
]

// Disable process selector warnings by default. Use debug profile to enable warnings.
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