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Test cases for configuration parsing
This PR adds two tests for yet not working cases. However, I was unable to fix them.
The first issue occurs if you define a method in a configuration file. The method is forgotten in the output.
Input: nextflow.config
process {
cpus = { getCpuValue() }
}
def getCpuValue() {
4
}
$ nextflow config nextflow.config
Output:
process {
cpus = { getCpuValue() }
}
The second issue is more complex. I broke down the configuration of nf-core/eager. If you have a three-level configuration structure, the third level ignores the renderClosureAsString
.
Inputs:
nextflow.config
profiles {
test { includeConfig 'nextflow2.config'}
}
nextflow2.config
includeConfig 'nextflow3.config'
nextflow3.config
params {
x = { 1 + 2 }
}
$ nextflow config nextflow.config -profile test
Output:
params {
x = Script45F3112A5F44215D3409D59317499615$_run_closure1$_closure2@f29353f
}
Both issues cause problems with the execution of some nf-core workflows.