crispr-process-nf/nextflow.config at master · ZuberLab/crispr-process-nf · GitHub

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/*
crispr-process-nf nextflow config
*/

params {
    inputDir = '01_raw'
    outputDir = 'results'
    library = 'library.txt'
	barcodes = 'barcodes.txt'
	barcode_demux_mismatches = 0
    barcode_length = 4
    demux_unknown = false
    random_barcode_length = 2
	spacer_seq = 'TTCCAGCATAGCTCTTAAAC'
    spacer_error_rate = 0.2
	max_guide_length = 21
    rc_guide_seq = false
	padding = 'GGT'
}


profiles {

    standard {
        includeConfig 'conf/resources.config'
    }

    apptainer {
        includeConfig 'conf/resources.config'
        includeConfig 'conf/apptainer.config'
    }

    cbe {
        includeConfig 'conf/resources.config'
        includeConfig 'conf/apptainer.config'
        includeConfig 'conf/cbe.config'
    }

    test {
        includeConfig 'conf/resources_test_mode.config'
        includeConfig 'conf/apptainer.config'
        includeConfig 'conf/cbe.config'
    }

}