Bug report
Expected behavior and actual behavior
I would like to directly run the output of these commands through a json parser.
Unfortunately, the output is not pure JSON, e.g.
nextflow inspect . -o json
Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/***
{
"processes": [
....
or
nextflow config -o json
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
{
"params": {
Steps to reproduce the problem
Create a minimal nextflow config e.g
params {
input = null
}
plugins {
id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
monochromeLogs = params.monochrome_logs
}
and run nextflow config -o json on it.
Program output
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
{
"params": {
"input": null
},
"plugins": [
"nf-schema@2.5.1"
],
"validation": {
"defaultIgnoreParams": [
"genomes"
],
"monochromeLogs": null
}
}
Environment
Version: 26.04.0 build 12031
System: Mac OS X 26.4.1
Runtime: Groovy 4.0.31 on OpenJDK 64-Bit Server VM 21.0.2+13-58
Additional context
I guess the source for both is different, but the general assumption I had is that i get pure json output in stdout when running -o json.
Bug report
Expected behavior and actual behavior
I would like to directly run the output of these commands through a json parser.
Unfortunately, the output is not pure JSON, e.g.
or
Steps to reproduce the problem
Create a minimal nextflow config e.g
params { input = null } plugins { id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs }and run
nextflow config -o jsonon it.Program output
Environment
Version: 26.04.0 build 12031
System: Mac OS X 26.4.1
Runtime: Groovy 4.0.31 on OpenJDK 64-Bit Server VM 21.0.2+13-58
Additional context
I guess the source for both is different, but the general assumption I had is that i get pure json output in stdout when running
-o json.