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schema.nf
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schema.nf
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#! /usr/bin/env nextflow
/*
*
* SCHEMA DEFINITION FOR PARAMS VALIDATION
*
*/
def Map schema = [:] // don't change this line
// --------------------------------------------------------------------------------------------------------------
schema.title1 = [title: 'GENERAL OPTIONS']
schema.min_nf_version = [value: '22.10.4', type: 'string', mandatory: true, allowed: '']
schema.publishmode = [value: 'copy', type: 'string', mandatory: true, allowed:['symlink', 'rellink', 'link', 'copy', 'copyNoFollow', 'move']]
schema.outdir = [value: "$launchDir/sc_preprocess_results/", type: 'string', mandatory: true]
schema.idx_outdir = [value: "${schema.outdir['value']}/alevin_idx/", type: 'string', mandatory: true]
schema.quant_outdir = [value: "${schema.outdir['value']}/alevin_quant/", type: 'string']
schema.mtx_outdir = [value: "${schema.outdir['value']}/mtx/", type: 'string', mandatory: true]
schema.pipe_dir = [value: "${schema.outdir['value']}/pipeline_info/", type: 'string', mandatory: true]
schema.qc_outdir = [value: "${schema.outdir['value']}/qc_dir/", type: 'string', mandatory: true]
schema.container = [value:'atpoint/sc_preprocess:v1.7.0', type:'string', mandatory:true]
schema.environment = [value: "$baseDir/environment.yml", type:'string', mandatory: true ]
schema.samplesheet = [value: '', type: 'string', pattern: /.*\.csv$/]
schema.title2 = [title: 'INDEXING OPTIONS']
schema.only_idx = [value: false, type: 'logical']
schema.idx = [value: '', type: 'string', mandatory: false]
schema.genome = [value: '', type: 'string', mandatory: false]
schema.gtf = [value: '', type: 'string', mandatory: false]
schema.gene_id = [value: 'gene_id', type: 'string', mandatory: true]
schema.gene_name = [value: 'gene_name', type: 'string', mandatory: true]
schema.read_length = [value: 150, type: 'numeric', mandatory: true]
schema.gene_type = [value: 'gene_type', type: 'string', mandatory: true]
schema.chrM = [value: 'chrM', type: 'string', mandatory: true]
schema.rrna = [value: 'rRNA', type: 'string', mandatory: true]
schema.idx_name = [value: 'idx_gentrome', type: 'string',]
schema.idx_args = [value: '--sparse', type: 'string']
schema.idx = [value: '', type: 'string']
schema.tgmap = [value: '', type: 'string']
schema.rrnagenes = [value: '', type: 'string']
schema.mtgenes = [value: '', type: 'string']
schema.features = [value: '', type: 'string']
schema.gene2type = [value: '', type: 'string']
schema.title3 = [title: 'QUANTIFICATION OPTIONS']
schema.r1_type = [value: '--bc-geometry 1[1-16] --umi-geometry 1[17-28]', type: 'string', mandatory: true]
schema.r2_type = [value: '--read-geometry 2[1-91]', type: 'string', mandatory: true]
schema.r2_type_fb = [value: '--read-geometry 2[11-25]', type: 'string', mandatory: true]
schema.quant_args = [value: '', type: 'string']
schema.quant_args_fb = [value: '', type: 'string']
schema.features_file = [value: '', type: 'string', mandatory: false]
schema.translate_barcodes = [value: false, type: 'logical']
schema.translate_list = [value: "", type: 'string']
// --------------------------------------------------------------------------------------------------------------
return schema // don't change this line