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Update nextflow.config #76

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Update nextflow.config #76

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11 changes: 9 additions & 2 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -190,8 +190,15 @@ env {
// Load Nextflow config for nf_aggregate workflow
includeConfig 'workflows/nf_aggregate/nextflow.config'

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