bin/

Save your custom scripts here. Ensure these scripts are executable. You can set the executable permission using:

chmod 770 <script_name>

In your main.nf or module/<process.nf> scripts, you can directly call the scripts placed in the bin/ directory as if they were any other command line tool. E.g. for module/example.nf, run a script called your_script.sh, example.nf would have to contain the following:

process example {
    input:
    path input_file

    output:
    path output_file

    script:
    """
    your_script.sh $input_file \
      > $output_file
    """
}

Example: custom samplesheet checker

In this template, we have used an example samplesheetchecker.py script which is executed by the process modules/check_input.nf. This script checks the input samplesheet.