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I would anticipate that passing arguments such as --minimap2_args '-k15' would result in the parameter minimap2_args being set to the string -k15. However, nextflow complains:
Unknown option: -k15 -- Check the available commands and options and syntax with 'help'
Note that the situation is different if the user provides --minimap2_args '-k 15'. The paramater is set to the string -k 15 as expected, so it is not simply that anything starting with '- is taken as an argument for nextflow itself.
Our users caught this as our documentation contains a CLI invocation built from the contents of the config file, we did not catch it in testing as our CI pipelines run nextflow -c config .... instead.
The text was updated successfully, but these errors were encountered:
Looks like the underlying CLI library (JCommander) prefers to parse -k15 as a CLI option instead of a parameter value. I believe this problem is solved by #3600 which adds a new CLI based on picocli, but ideally i would want to refactor the existing CLI to also use picocli, which would solve the problem here.
Bug report
Expected behavior and actual behavior
I would anticipate that passing arguments such as
--minimap2_args '-k15'
would result in the parameterminimap2_args
being set to the string-k15
. However, nextflow complains:Note that the situation is different if the user provides
--minimap2_args '-k 15'
. The paramater is set to the string-k 15
as expected, so it is not simply that anything starting with'-
is taken as an argument for nextflow itself.Steps to reproduce the problem
Program output
There's no nextflow.log produced.
Environment
Additional context
There's a difference in behaviour compared to when the arguments are provided in a config file as:
Our users caught this as our documentation contains a CLI invocation built from the contents of the config file, we did not catch it in testing as our CI pipelines run
nextflow -c config ....
instead.The text was updated successfully, but these errors were encountered: