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🚨 solve linter issues related to VScode and nextflow languageserver #87

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Feb 3, 2025
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🐛 fix process.shell in nextflow.config
support nextflow >= 24.10.4
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bunop committed Jan 22, 2025
commit c2b05d52c742f17145066d0b748c213dc8d4f40e
15 changes: 7 additions & 8 deletions nextflow.config
Original file line number Diff line number Diff line change
@@ -145,14 +145,13 @@ 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
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