Expected behavior:
When running a workflow with a -params-file in json format, I expect the params property to contain only the provided keys set in the json file.
Actual behavior:
While the key (and values) set in the parameters file are accessible through the params property to the workflow, additional parameters are being added with a key derived from the original one.
This only happens if the parameter are named using camel case and/or kebab case naming conventions (i.e. camelCase, kebab-case).
When setting a parameter named testParam nextflow will add an additional test-param parameter to params property that was not present in the file.
N E X T F L O W ~ version 22.10.2
Launching `main.nf` [lethal_laplace] DSL2 - revision: 47784e7723
Params map: [camelCase:test, camel-case:test, kebab-case:test, kebabCase:test, normal:test]
Notice that the camel case and kebab case parameters are duplicated while the "normal" parameter is not.
Should be addressed by #4702 . Any kebab-case param from the CLI should be converted to camelCase and not stored, since kebab case params can't be accessed from the script anyway
Bug report
Expected behavior and actual behavior
Expected behavior: When running a workflow with a
-params-file
injson
format, I expect theparams
property to contain only the provided keys set in thejson
file.Actual behavior: While the key (and values) set in the parameters file are accessible through the
params
property to the workflow, additional parameters are being added with a key derived from the original one. This only happens if the parameter are named using camel case and/or kebab case naming conventions (i.e.camelCase
,kebab-case
). When setting a parameter namedtestParam
nextflow will add an additionaltest-param
parameter toparams
property that was not present in the file.Steps to reproduce the problem
Create nextflow and parameters file:
main.nf:
params.json:
Run the nf file with the parameters file:
Program output
Notice that the camel case and kebab case parameters are duplicated while the "normal" parameter is not.
Environment