how do I enable nextflow to read scripts in bin folder?

[complexgenome]

Hi there, I've a python script in a bin folder. I try to run it, however, nextflow says script not found.

process test {

    maxForks 3
        debug true
        errorStrategy 'retry'
    maxRetries 2
publishDir path: "/data1/users/sanjeev/nextflow/learn_nextflow/", mode: 'copy' 
output:
stdout
    script:
    """
echo "hello"
python2 parse_cnvs_V2.py
    """
}

workflow {

    test()
}

nextflow run test.nf

I get error as:

Command error:
  hello
  python2: can't open file 'parse_cnvs_V2.py': [Errno 2] No such file or directory

How do I have nextflow pick script from the bin folder created?

[bentsherman]

You have to add a shebang (#!/user/bin/env python2) to the first line of your python script, make it executable, and execute it directly in your process:

    """
    echo "hello"
    parse_cnvs_V2.py
    """

[complexgenome]

ah, wonderful. Thank you for your reply. It worked.