How to capture arguments from command line argument in workflow

[yamaura]

Hi!

I want to capture value from arguments not options.
This helps me to launch workflow with following commands:

$ nextflow test.nf --test arg1 read{1,2}.fq

I can catch arg1 value with params.test.
But how to capture the values raed1.fq and read2.fq?

Thanks

[mribeirodantas]

If you want to provide several values to a parameter in Nextflow, you can either wrap them with quotes or concatenate them with a comma. See the examples below:

example.nf

println params.example

You can run this Nextflow script in the two ways below to get all values:

nextflow run example.nf --example test1,test2,test3
# OR
nextflow run example.nf --example "test1 test2 test3"

Output:

➜  ~ nextflow run example.nf --example "test test2 test3"
N E X T F L O W  ~  version 22.10.4
Launching `ex.nf` [scruffy_payne] DSL2 - revision: a982a55670
test test2 test3

Or

➜  ~ nextflow run example.nf --example test,test2,test3
N E X T F L O W  ~  version 22.10.4
Launching `ex.nf` [tender_heyrovsky] DSL2 - revision: a982a55670
test,test2,test3

You should also check the -params-file argument of the Nextflow CLI. You can provide a JSON/YAML file to it and access the fields within your Nextflow script. For example, let's replace our example.nf file with the following content:

println params.example1
println params.example2

And then create a file named my_params.json with the following content:

{
  "example1": "Test 1",
  "example2": "Test 2"
}

Now, when we run nextflow run example.nf -params-file my_params.json I will get:

➜  ~ nextflow run ex.nf -params-file my_params.json
N E X T F L O W  ~  version 22.10.4
Launching `ex.nf` [boring_bhaskara] DSL2 - revision: b4dc14b49e
Test 1
Test 2

[pditommaso]

or just use the args implicit variable using the first command line

For example having test.nf as:

println "test: $params.test"
println "args: $args"

» nextflow run test.nf --test arg1 read{1,2}.fq
N E X T F L O W  ~  version 22.12.0-edge
Launching `test.nf` [deadly_jones] DSL2 - revision: 75203f325f
test: arg1
args: [read1.fq, read2.fq]

[mribeirodantas]

That's a new one for me! That's nice! Do you have a good use case in mind? Or know of anyone using it to do something cool?

Also, can I separate it between parameters?

➜  ~ nextflow run ex.nf --example1 test1 blah blah --example2 test2 bleh bleh   
N E X T F L O W  ~  version 22.10.4
Launching `ex.nf` [sharp_swanson] DSL2 - revision: 439718d4f5
test1
test2
[blah, blah, bleh, bleh]

I would like to get a list with blah, blah and another one with bleh, bleh.

[pditommaso]

args is just an array holding all unnamed cli parameters. therefore you can args[0] to access therfirst, args[1] the second, .. etc

[mribeirodantas]

Oh, OK. Now I get how it works. Thanks 😄

[yamaura]

Thank you, It is what I wanted to know!