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Description
Bug report
Expected behavior and actual behavior
When I use a withName process selector that has special characters (e.g. '.*TASK.*'), I get a warning about unknown config options:
e.g.
WARN: Unrecognized config option 'process.*TASK.*.ext.args'
Steps to reproduce the problem
main.nf
workflow {
TASK(1).view()
}
process TASK {
input:
val thing
output:
stdout
script:
def args = task.ext.args ?: 'nothing'
def prefix = task.ext.prefix ?: 'default'
"""
echo "${thing} ${args}" | tee "${prefix}.txt"
"""
}
nextflow.config
resume = true
process {
withName: '.*TASK.*' {
ext.args = 'hello'
ext.prefix = 'prefix'
}
}
command
NXF_SYNTAX_PARSER=v2 nextflow run .
The issue goes away if the special chars are removed from the withName selector. For example, if the nextflow.config is replaced by this:
resume = true
process {
withName: 'TASK' {
ext.args = 'hello'
ext.prefix = 'prefix'
}
}
Program output
N E X T F L O W ~ version 25.10.0
Launching `main.nf` [exotic_torricelli] DSL2 - revision: eeea9e75bc
WARN: Unrecognized config option 'process.*TASK.*.ext.args'
WARN: Unrecognized config option 'process.*TASK.*.ext.prefix'
executor > local (1)
[b0/34fb22] process > TASK [100%] 1 of 1 ✔
1 hello
Environment
- Nextflow version: 25.10.0 with NXF_SYNTAX_PARSER=v2
- Java version: 21.0.2
- Operating system: macOS
- Bash version: GNU bash, version 3.2.57(1)-release (arm64-apple-darwin25)