How to run Python Script in Nextflow

user_13165120 0
Viewed 2821

I'm new to Nextflow and I tried to run a Python Script in Nextflow. So I stored the Python Script in the same Folder as the Nextflow Pipeline and tried to run it but I always get this error: .command.sh: line 2: ./example.py: No such file or directory. Does anybody encountered the same problem and was capable to solve it?

My Process looks like this:

#!/usr/bin/env nextflow

input_ch = Channel.fromPath('data/*.txt')

process foo {

    input:
    file x from input_ch

    output:
    file "$x" into outputt_ch

    """
    ./example.py ${x}
    """

}

P.S.:My Python Script is executable from the Terminal!

Thank you in advance!

nextflow workflow python-3.x
2 Answers

Nextflow runs each task in a separate working directory. Therefore ./example.py won't work. You have to use example.py and make the script accessible through the system PATH or copy it into the project bin/ directory.

user_3959210

Another solution is to use the projectDir variable. For example,

#!/usr/bin/env nextflow

input_ch = Channel.fromPath('data/*.txt')
project_dir = projectDir

process foo {

    input:
    file x from input_ch

    output:
    file "$x" into outputt_ch

    """
    python $project_dir/example.py ${x}
    """

}
user_89935620
Related