Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.6.1/lib/help/fastp.nf @ 11:749faef1caa9

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
parents
children
rev   line source
kkonganti@11 1 // Help text for fastp within CPIPES.
kkonganti@11 2
kkonganti@11 3 def fastpHelp(params) {
kkonganti@11 4
kkonganti@11 5 Map tool = [:]
kkonganti@11 6 Map toolspecs = [:]
kkonganti@11 7 tool.text = [:]
kkonganti@11 8 tool.helpparams = [:]
kkonganti@11 9
kkonganti@11 10 toolspecs = [
kkonganti@11 11 'fastp_run': [
kkonganti@11 12 clihelp: 'Run fastp tool. Default: ' +
kkonganti@11 13 (params.fastp_run ?: false),
kkonganti@11 14 cliflag: null,
kkonganti@11 15 clivalue: null
kkonganti@11 16 ],
kkonganti@11 17 'fastp_failed_out': [
kkonganti@11 18 clihelp: 'Specify whether to store reads that cannot pass the filters. ' +
kkonganti@11 19 "Default: ${params.fastp_failed_out}",
kkonganti@11 20 cliflag: null,
kkonganti@11 21 clivalue: null
kkonganti@11 22 ],
kkonganti@11 23 'fastp_merged_out': [
kkonganti@11 24 clihelp: 'Specify whether to store merged output or not. ' +
kkonganti@11 25 "Default: ${params.fastp_merged_out}",
kkonganti@11 26 cliflag: null,
kkonganti@11 27 clivalue: null
kkonganti@11 28 ],
kkonganti@11 29 'fastp_overlapped_out': [
kkonganti@11 30 clihelp: 'For each read pair, output the overlapped region if it has no mismatched base. ' +
kkonganti@11 31 "Default: ${params.fastp_overlapped_out}",
kkonganti@11 32 cliflag: '--overlapped_out',
kkonganti@11 33 clivalue: (params.fastp_overlapped_out ?: '')
kkonganti@11 34 ],
kkonganti@11 35 'fastp_6': [
kkonganti@11 36 clihelp: "Indicate that the input is using phred64 scoring (it'll be converted to phred33, " +
kkonganti@11 37 'so the output will still be phred33). ' +
kkonganti@11 38 "Default: ${params.fastp_6}",
kkonganti@11 39 cliflag: '-6',
kkonganti@11 40 clivalue: (params.fastp_6 ? ' ' : '')
kkonganti@11 41 ],
kkonganti@11 42 'fastp_reads_to_process': [
kkonganti@11 43 clihelp: 'Specify how many reads/pairs are to be processed. Default value 0 means ' +
kkonganti@11 44 'process all reads. ' +
kkonganti@11 45 "Default: ${params.fastp_reads_to_process}",
kkonganti@11 46 cliflag: '--reads_to_process',
kkonganti@11 47 clivalue: (params.fastp_reads_to_process ?: '')
kkonganti@11 48 ],
kkonganti@11 49 'fastp_fix_mgi_id': [
kkonganti@11 50 clihelp: 'The MGI FASTQ ID format is not compatible with many BAM operation tools, ' +
kkonganti@11 51 'enable this option to fix it. ' +
kkonganti@11 52 "Default: ${params.fastp_fix_mgi_id}",
kkonganti@11 53 cliflag: '--fix_mgi_id',
kkonganti@11 54 clivalue: (params.fastp_fix_mgi_id ? ' ' : '')
kkonganti@11 55 ],
kkonganti@11 56 'fastp_A': [
kkonganti@11 57 clihelp: 'Disable adapter trimming. On by default. ' +
kkonganti@11 58 "Default: ${params.fastp_A}",
kkonganti@11 59 cliflag: '-A',
kkonganti@11 60 clivalue: (params.fastp_A ? ' ' : '')
kkonganti@11 61 ],
kkonganti@11 62 'fastp_adapter_fasta': [
kkonganti@11 63 clihelp: 'Specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences ' +
kkonganti@11 64 'in this FASTA file. ' +
kkonganti@11 65 "Default: ${params.fastp_adapter_fasta}",
kkonganti@11 66 cliflag: '--adapter_fasta',
kkonganti@11 67 clivalue: (params.fastp_adapter_fasta ?: '')
kkonganti@11 68 ],
kkonganti@11 69 'fastp_f': [
kkonganti@11 70 clihelp: 'Trim how many bases in front of read1. ' +
kkonganti@11 71 "Default: ${params.fastp_f}",
kkonganti@11 72 cliflag: '-f',
kkonganti@11 73 clivalue: (params.fastp_f ?: '')
kkonganti@11 74 ],
kkonganti@11 75 'fastp_t': [
kkonganti@11 76 clihelp: 'Trim how many bases at the end of read1. ' +
kkonganti@11 77 "Default: ${params.fastp_t}",
kkonganti@11 78 cliflag: '-t',
kkonganti@11 79 clivalue: (params.fastp_t ?: '')
kkonganti@11 80 ],
kkonganti@11 81 'fastp_b': [
kkonganti@11 82 clihelp: 'Max length of read1 after trimming. ' +
kkonganti@11 83 "Default: ${params.fastp_b}",
kkonganti@11 84 cliflag: '-b',
kkonganti@11 85 clivalue: (params.fastp_b ?: '')
kkonganti@11 86 ],
kkonganti@11 87 'fastp_F': [
kkonganti@11 88 clihelp: 'Trim how many bases in front of read2. ' +
kkonganti@11 89 "Default: ${params.fastp_F}",
kkonganti@11 90 cliflag: '-F',
kkonganti@11 91 clivalue: (params.fastp_F ?: '')
kkonganti@11 92 ],
kkonganti@11 93 'fastp_T': [
kkonganti@11 94 clihelp: 'Trim how many bases at the end of read2. ' +
kkonganti@11 95 "Default: ${params.fastp_T}",
kkonganti@11 96 cliflag: '-T',
kkonganti@11 97 clivalue: (params.fastp_T ?: '')
kkonganti@11 98 ],
kkonganti@11 99 'fastp_B': [
kkonganti@11 100 clihelp: 'Max length of read2 after trimming. ' +
kkonganti@11 101 "Default: ${params.fastp_B}",
kkonganti@11 102 cliflag: '-B',
kkonganti@11 103 clivalue: (params.fastp_B ?: '')
kkonganti@11 104 ],
kkonganti@11 105 'fastp_dedup': [
kkonganti@11 106 clihelp: 'Enable deduplication to drop the duplicated reads/pairs. ' +
kkonganti@11 107 "Default: ${params.fastp_dedup}",
kkonganti@11 108 cliflag: '--dedup',
kkonganti@11 109 clivalue: (params.fastp_dedup ? ' ' : '')
kkonganti@11 110 ],
kkonganti@11 111 'fastp_dup_calc_accuracy': [
kkonganti@11 112 clihelp: 'Accuracy level to calculate duplication (1~6), higher level uses more memory ' +
kkonganti@11 113 '(1G, 2G, 4G, 8G, 16G, 24G). Default 1 for no-dedup mode, and 3 for dedup mode. ' +
kkonganti@11 114 "Default: ${params.fastp_dup_calc_accuracy}",
kkonganti@11 115 cliflag: '--dup_calc_accuracy',
kkonganti@11 116 clivalue: (params.fastp_dup_calc_accuracy ?: '')
kkonganti@11 117 ],
kkonganti@11 118 'fastp_poly_g_min_len': [
kkonganti@11 119 clihelp: 'The minimum length to detect polyG in the read tail. ' +
kkonganti@11 120 "Default: ${params.fastp_poly_g_min_len}",
kkonganti@11 121 cliflag: '--poly_g_min_len',
kkonganti@11 122 clivalue: (params.fastp_poly_g_min_len ?: '')
kkonganti@11 123 ],
kkonganti@11 124 'fastp_G': [
kkonganti@11 125 clihelp: 'Disable polyG tail trimming. ' +
kkonganti@11 126 "Default: ${params.fastp_G}",
kkonganti@11 127 cliflag: '-G',
kkonganti@11 128 clivalue: (params.fastp_G ? ' ' : '')
kkonganti@11 129 ],
kkonganti@11 130 'fastp_x': [
kkonganti@11 131 clihelp: "Enable polyX trimming in 3' ends. " +
kkonganti@11 132 "Default: ${params.fastp_x}",
kkonganti@11 133 cliflag: 'x=',
kkonganti@11 134 clivalue: (params.fastp_x ? ' ' : '')
kkonganti@11 135 ],
kkonganti@11 136 'fastp_poly_x_min_len': [
kkonganti@11 137 clihelp: 'The minimum length to detect polyX in the read tail. ' +
kkonganti@11 138 "Default: ${params.fastp_poly_x_min_len}",
kkonganti@11 139 cliflag: '--poly_x_min_len',
kkonganti@11 140 clivalue: (params.fastp_poly_x_min_len ?: '')
kkonganti@11 141 ],
kkonganti@11 142 'fastp_cut_front': [
kkonganti@11 143 clihelp: "Move a sliding window from front (5') to tail, drop the bases in the window " +
kkonganti@11 144 'if its mean quality < threshold, stop otherwise. ' +
kkonganti@11 145 "Default: ${params.fastp_cut_front}",
kkonganti@11 146 cliflag: '--cut_front',
kkonganti@11 147 clivalue: (params.fastp_cut_front ? ' ' : '')
kkonganti@11 148 ],
kkonganti@11 149 'fastp_cut_tail': [
kkonganti@11 150 clihelp: "Move a sliding window from tail (3') to front, drop the bases in the window " +
kkonganti@11 151 'if its mean quality < threshold, stop otherwise. ' +
kkonganti@11 152 "Default: ${params.fastp_cut_tail}",
kkonganti@11 153 cliflag: '--cut_tail',
kkonganti@11 154 clivalue: (params.fastp_cut_tail ? ' ' : '')
kkonganti@11 155 ],
kkonganti@11 156 'fastp_cut_right': [
kkonganti@11 157 clihelp: "Move a sliding window from tail, drop the bases in the window and the right part " +
kkonganti@11 158 'if its mean quality < threshold, and then stop. ' +
kkonganti@11 159 "Default: ${params.fastp_cut_right}",
kkonganti@11 160 cliflag: '--cut_right',
kkonganti@11 161 clivalue: (params.fastp_cut_right ? ' ' : '')
kkonganti@11 162 ],
kkonganti@11 163 'fastp_W': [
kkonganti@11 164 clihelp: "Sliding window size shared by --fastp_cut_front, --fastp_cut_tail and " +
kkonganti@11 165 '--fastp_cut_right. ' +
kkonganti@11 166 "Default: ${params.fastp_W}",
kkonganti@11 167 cliflag: '--cut_window_size',
kkonganti@11 168 clivalue: (params.fastp_W ?: '')
kkonganti@11 169 ],
kkonganti@11 170 'fastp_M': [
kkonganti@11 171 clihelp: "The mean quality requirement shared by --fastp_cut_front, --fastp_cut_tail and " +
kkonganti@11 172 '--fastp_cut_right. ' +
kkonganti@11 173 "Default: ${params.fastp_M}",
kkonganti@11 174 cliflag: '--cut_mean_quality',
kkonganti@11 175 clivalue: (params.fastp_M ?: '')
kkonganti@11 176 ],
kkonganti@11 177 'fastp_q': [
kkonganti@11 178 clihelp: 'The quality value below which a base should is not qualified. ' +
kkonganti@11 179 "Default: ${params.fastp_q}",
kkonganti@11 180 cliflag: '-q',
kkonganti@11 181 clivalue: (params.fastp_q ?: '')
kkonganti@11 182 ],
kkonganti@11 183 'fastp_u': [
kkonganti@11 184 clihelp: 'What percent of bases are allowed to be unqualified. ' +
kkonganti@11 185 "Default: ${params.fastp_u}",
kkonganti@11 186 cliflag: '-u',
kkonganti@11 187 clivalue: (params.fastp_u ?: '')
kkonganti@11 188 ],
kkonganti@11 189 'fastp_n': [
kkonganti@11 190 clihelp: "How many N's can a read have. " +
kkonganti@11 191 "Default: ${params.fastp_n}",
kkonganti@11 192 cliflag: '-n',
kkonganti@11 193 clivalue: (params.fastp_n ?: '')
kkonganti@11 194 ],
kkonganti@11 195 'fastp_e': [
kkonganti@11 196 clihelp: "If the full reads' average quality is below this value, then it is discarded. " +
kkonganti@11 197 "Default: ${params.fastp_e}",
kkonganti@11 198 cliflag: '-e',
kkonganti@11 199 clivalue: (params.fastp_e ?: '')
kkonganti@11 200 ],
kkonganti@11 201 'fastp_l': [
kkonganti@11 202 clihelp: 'Reads shorter than this length will be discarded. ' +
kkonganti@11 203 "Default: ${params.fastp_l}",
kkonganti@11 204 cliflag: '-l',
kkonganti@11 205 clivalue: (params.fastp_l ?: '')
kkonganti@11 206 ],
kkonganti@11 207 'fastp_max_len': [
kkonganti@11 208 clihelp: 'Reads longer than this length will be discarded. ' +
kkonganti@11 209 "Default: ${params.fastp_max_len}",
kkonganti@11 210 cliflag: '--length_limit',
kkonganti@11 211 clivalue: (params.fastp_max_len ?: '')
kkonganti@11 212 ],
kkonganti@11 213 'fastp_y': [
kkonganti@11 214 clihelp: 'Enable low complexity filter. The complexity is defined as the percentage ' +
kkonganti@11 215 'of bases that are different from its next base (base[i] != base[i+1]). ' +
kkonganti@11 216 "Default: ${params.fastp_y}",
kkonganti@11 217 cliflag: '-y',
kkonganti@11 218 clivalue: (params.fastp_y ? ' ' : '')
kkonganti@11 219 ],
kkonganti@11 220 'fastp_Y': [
kkonganti@11 221 clihelp: 'The threshold for low complexity filter (0~100). Ex: A value of 30 means ' +
kkonganti@11 222 '30% complexity is required. ' +
kkonganti@11 223 "Default: ${params.fastp_Y}",
kkonganti@11 224 cliflag: '-Y',
kkonganti@11 225 clivalue: (params.fastp_Y ?: '')
kkonganti@11 226 ],
kkonganti@11 227 'fastp_U': [
kkonganti@11 228 clihelp: 'Enable Unique Molecular Identifier (UMI) pre-processing. ' +
kkonganti@11 229 "Default: ${params.fastp_U}",
kkonganti@11 230 cliflag: '-U',
kkonganti@11 231 clivalue: (params.fastp_U ? ' ' : '')
kkonganti@11 232 ],
kkonganti@11 233 'fastp_umi_loc': [
kkonganti@11 234 clihelp: 'Specify the location of UMI, can be one of ' +
kkonganti@11 235 'index1/index2/read1/read2/per_index/per_read. ' +
kkonganti@11 236 "Default: ${params.fastp_umi_loc}",
kkonganti@11 237 cliflag: '--umi_loc',
kkonganti@11 238 clivalue: (params.fastp_umi_loc ?: '')
kkonganti@11 239 ],
kkonganti@11 240 'fastp_umi_len': [
kkonganti@11 241 clihelp: 'If the UMI is in read1 or read2, its length should be provided. ' +
kkonganti@11 242 "Default: ${params.fastp_umi_len}",
kkonganti@11 243 cliflag: '--umi_len',
kkonganti@11 244 clivalue: (params.fastp_umi_len ?: '')
kkonganti@11 245 ],
kkonganti@11 246 'fastp_umi_prefix': [
kkonganti@11 247 clihelp: 'If specified, an underline will be used to connect prefix and UMI ' +
kkonganti@11 248 '(i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). ' +
kkonganti@11 249 "Default: ${params.fastp_umi_prefix}",
kkonganti@11 250 cliflag: '--umi_prefix',
kkonganti@11 251 clivalue: (params.fastp_umi_prefix ?: '')
kkonganti@11 252 ],
kkonganti@11 253 'fastp_umi_skip': [
kkonganti@11 254 clihelp: 'If the UMI is in read1 or read2, fastp can skip several bases following the UMI. ' +
kkonganti@11 255 "Default: ${params.fastp_umi_skip}",
kkonganti@11 256 cliflag: '--umi_skip',
kkonganti@11 257 clivalue: (params.fastp_umi_skip ?: '')
kkonganti@11 258 ],
kkonganti@11 259 'fastp_p': [
kkonganti@11 260 clihelp: 'Enable overrepresented sequence analysis. ' +
kkonganti@11 261 "Default: ${params.fastp_p}",
kkonganti@11 262 cliflag: '-p',
kkonganti@11 263 clivalue: (params.fastp_p ? ' ' : '')
kkonganti@11 264 ],
kkonganti@11 265 'fastp_P': [
kkonganti@11 266 clihelp: 'One in this many number of reads will be computed for overrepresentation analysis ' +
kkonganti@11 267 '(1~10000), smaller is slower. ' +
kkonganti@11 268 "Default: ${params.fastp_P}",
kkonganti@11 269 cliflag: '-P',
kkonganti@11 270 clivalue: (params.fastp_P ?: '')
kkonganti@11 271 ]
kkonganti@11 272 ]
kkonganti@11 273
kkonganti@11 274 toolspecs.each {
kkonganti@11 275 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@11 276 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@11 277 }
kkonganti@11 278
kkonganti@11 279 return tool
kkonganti@11 280 }