Hi there. I need to use the --reverse-complement flag with Mageck count. I wonder if you could add this to the pipeline?

Hi @Adam Reid, you can use a config file to provide extra arguments. In your config file you can add this

process {
    withName: MAGECK_COUNT {
        ext.args = '--reverse-complement'
    }
}

And you can provide it when running the pipeline with

nextflow run nf-core/crisprseq -params-file my_config.config