kkonganti@1: // Help text for flye within CPIPES.
kkonganti@1: 
kkonganti@1: def flyeHelp(params) {
kkonganti@1: 
kkonganti@1:     Map tool = [:]
kkonganti@1:     Map toolspecs = [:]
kkonganti@1:     tool.text = [:]
kkonganti@1:     tool.helpparams = [:]
kkonganti@1: 
kkonganti@1:     toolspecs = [
kkonganti@1:         'flye_pacbio_raw': [
kkonganti@1:             clihelp: 'Input FASTQ reads are PacBio regular CLR reads (<20% error) ' +
kkonganti@1:                 "Default: ${params.flye_pacbio_raw}",
kkonganti@1:             cliflag: '--pacbio-raw',
kkonganti@1:             clivalue: (params.flye_pacbio_raw ? ' ' : '')
kkonganti@1:         ], 
kkonganti@1:         'flye_pacbio_corr': [
kkonganti@1:             clihelp: 'Input FASTQ reads are PacBio reads that were corrected ' +
kkonganti@1:                 "with other methods (<3% error). Default: ${params.flye_pacbio_corr}",
kkonganti@1:             cliflag: '--pacbio-corr',
kkonganti@1:             clivalue: (params.flye_pacbio_corr ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'flye_pacbio_hifi': [
kkonganti@1:             clihelp: 'Input FASTQ reads are PacBio HiFi reads (<1% error). ' +
kkonganti@1:                 "Default: ${params.flye_pacbio_hifi}",
kkonganti@1:             cliflag: '--pacbio-hifi',
kkonganti@1:             clivalue: (params.flye_pacbio_hifi ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'flye_nano_raw': [
kkonganti@1:             clihelp: 'Input FASTQ reads are ONT regular reads, pre-Guppy5 (<20% error). ' +
kkonganti@1:                 "Default: ${params.flye_nano_raw}",
kkonganti@1:             cliflag: '--nano-raw',
kkonganti@1:             clivalue: (params.flye_nano_raw ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'flye_nano_corr': [
kkonganti@1:             clihelp: 'Input FASTQ reads are ONT reads that were corrected with other ' +
kkonganti@1:                 "methods (<3% error). Default: ${params.flye_nano_corr}",
kkonganti@1:             cliflag: '--nano-corr',
kkonganti@1:             clivalue: (params.flye_nano_corr ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'flye_nano_hq': [
kkonganti@1:             clihelp: 'Input FASTQ reads are ONT high-quality reads: ' +
kkonganti@1:                 "Guppy5+ SUP or Q20 (<5% error). Default: ${params.flye_nano_hq}",
kkonganti@1:             cliflag: '--nano-hq',
kkonganti@1:             clivalue: (params.flye_nano_hq ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'flye_genome_size': [
kkonganti@1:             clihelp: 'Estimated genome size (for example, 5m or 2.6g). ' +
kkonganti@1:                 "Default: ${params.flye_genome_size}",
kkonganti@1:             cliflag: '--genome-size',
kkonganti@1:             clivalue: (params.flye_genome_size ?: '')
kkonganti@1:         ],
kkonganti@1:         'flye_polish_iter': [
kkonganti@1:             clihelp: 'Number of genome polishing iterations. ' +
kkonganti@1:                 "Default: ${params.flye_polish_iter}",
kkonganti@1:             cliflag: '--iterations',
kkonganti@1:             clivalue: (params.flye_polish_iter ?: '')
kkonganti@1:         ],
kkonganti@1:         'flye_meta': [
kkonganti@1:             clihelp: "Do a metagenome assembly (unenven coverage mode). Default: ${params.flye_meta}",
kkonganti@1:             cliflag: '--meta',
kkonganti@1:             clivalue: (params.flye_meta ? ' ' : '')
kkonganti@1:         ],
kkonganti@1:         'flye_min_overlap': [
kkonganti@1:             clihelp: "Minimum overlap between reads. Default: ${params.flye_min_overlap}",
kkonganti@1:             cliflag: '--min-overlap',
kkonganti@1:             clivalue: (params.flye_min_overlap ?: '')
kkonganti@1:         ],
kkonganti@1:         'flye_scaffold': [
kkonganti@1:             clihelp: "Enable scaffolding using assembly graph. Default: ${params.flye_scaffold}",
kkonganti@1:             cliflag: '--scaffold',
kkonganti@1:             clivalue: (params.flye_scaffold ? ' ' : '')
kkonganti@1:         ]
kkonganti@1:     ]
kkonganti@1: 
kkonganti@1:     toolspecs.each {
kkonganti@1:         k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@1:         tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@1:     }
kkonganti@1: 
kkonganti@1:     return tool
kkonganti@1: }