Include groovy-cli into dependencies

[ssadedin]

New feature

Nextflow currently includes a number of useful Groovy core libraries that enable various native Groovy functions to be used in building pipeline scripts.

I would like to propose that one of the groovy-cli modules be added. I think perhaps the more light weight cli-commons module might be more appropriate as I'm sure there is a strong desire to keep the Nextflow download light weight.

Why I'm suggesting this

One of the nice features of Bpipe that I miss in Nextflow is built in options parsing. In Bpipe, you can very easily make the pipeline consume arguments such as flags, validate their types and provide comprehensive help output, because this is all built into Groovy.

Usage scenario

This feature would enable people to easily build in sophisticated argument parsing and help for their Nextflow pipelines.

Suggest implementation

You don't need to do anything, simply add one of the groovy-cli modules as a dependency. Then users can write things like

cli = new CliBuilder(usage:'My fancy pipeline').tap {
   my_option 'This option is very important', args: 1, required: true
}
options = cli.parse(args)

println "Running the pipeline with the option $options.my_option"

and they can run it with Nextflow like:

./nextflow my_pipeline.nf -my_option the_option_value

NB: I know users can accomplish this themselves with Groovy but I feel it's a really nice benefit in this case to have it built in.

[pditommaso]

Not sure I'm missing something, but nextflow has built-in options parsing as well.

Just try

cat <<EOT >> hello.nf
params.foo = 'Hello world'
println params.foo
EOT

then run

nextflow run hello.nf --foo Hola

[pditommaso]

Closing for lack of activity

[cerebis]

An old issue, but every time sit down to nextflow -- and think about offering users a robust interface -- it perhaps evokes the same thought as motivated @ssadedin to post a feature request.

Sure, Nextflow has basic abilities to parse arguments but you cannot define a CLI and validate it. I've just been studying nf-core again, in hopes that they have solved this issue. Their CLIs are very nice by Nextflow standards, but seem to be hand-crafted in each case.

I would point to Python's argparse or the much older Apache Java commnons-cli as examples.

[bentsherman]

We are discussing an overhaul of pipeline params, including the validation of CLI params against a schema: #4669

Feel free to share your thoughts there, I have also sketched out a few ideas