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comparison 0.5.0/lib/help/fastp.nf @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 // Help text for fastp within CPIPES.
2
3 def fastpHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'fastp_run': [
12 clihelp: 'Run fastp tool. Default: ' +
13 (params.fastp_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'fastp_failed_out': [
18 clihelp: 'Specify whether to store reads that cannot pass the filters. ' +
19 "Default: ${params.fastp_failed_out}",
20 cliflag: null,
21 clivalue: null
22 ],
23 'fastp_merged_out': [
24 clihelp: 'Specify whether to store merged output or not. ' +
25 "Default: ${params.fastp_merged_out}",
26 cliflag: null,
27 clivalue: null
28 ],
29 'fastp_overlapped_out': [
30 clihelp: 'For each read pair, output the overlapped region if it has no mismatched base. ' +
31 "Default: ${params.fastp_overlapped_out}",
32 cliflag: '--overlapped_out',
33 clivalue: (params.fastp_overlapped_out ?: '')
34 ],
35 'fastp_6': [
36 clihelp: "Indicate that the input is using phred64 scoring (it'll be converted to phred33, " +
37 'so the output will still be phred33). ' +
38 "Default: ${params.fastp_6}",
39 cliflag: '-6',
40 clivalue: (params.fastp_6 ? ' ' : '')
41 ],
42 'fastp_reads_to_process': [
43 clihelp: 'Specify how many reads/pairs are to be processed. Default value 0 means ' +
44 'process all reads. ' +
45 "Default: ${params.fastp_reads_to_process}",
46 cliflag: '--reads_to_process',
47 clivalue: (params.fastp_reads_to_process ?: '')
48 ],
49 'fastp_fix_mgi_id': [
50 clihelp: 'The MGI FASTQ ID format is not compatible with many BAM operation tools, ' +
51 'enable this option to fix it. ' +
52 "Default: ${params.fastp_fix_mgi_id}",
53 cliflag: '--fix_mgi_id',
54 clivalue: (params.fastp_fix_mgi_id ? ' ' : '')
55 ],
56 'fastp_A': [
57 clihelp: 'Disable adapter trimming. On by default. ' +
58 "Default: ${params.fastp_A}",
59 cliflag: '-A',
60 clivalue: (params.fastp_A ? ' ' : '')
61 ],
62 'fastp_adapter_fasta': [
63 clihelp: 'Specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences ' +
64 'in this FASTA file. ' +
65 "Default: ${params.fastp_adapter_fasta}",
66 cliflag: '--adapter_fasta',
67 clivalue: (params.fastp_adapter_fasta ?: '')
68 ],
69 'fastp_f': [
70 clihelp: 'Trim how many bases in front of read1. ' +
71 "Default: ${params.fastp_f}",
72 cliflag: '-f',
73 clivalue: (params.fastp_f ?: '')
74 ],
75 'fastp_t': [
76 clihelp: 'Trim how many bases at the end of read1. ' +
77 "Default: ${params.fastp_t}",
78 cliflag: '-t',
79 clivalue: (params.fastp_t ?: '')
80 ],
81 'fastp_b': [
82 clihelp: 'Max length of read1 after trimming. ' +
83 "Default: ${params.fastp_b}",
84 cliflag: '-b',
85 clivalue: (params.fastp_b ?: '')
86 ],
87 'fastp_F': [
88 clihelp: 'Trim how many bases in front of read2. ' +
89 "Default: ${params.fastp_F}",
90 cliflag: '-F',
91 clivalue: (params.fastp_F ?: '')
92 ],
93 'fastp_T': [
94 clihelp: 'Trim how many bases at the end of read2. ' +
95 "Default: ${params.fastp_T}",
96 cliflag: '-T',
97 clivalue: (params.fastp_T ?: '')
98 ],
99 'fastp_B': [
100 clihelp: 'Max length of read2 after trimming. ' +
101 "Default: ${params.fastp_B}",
102 cliflag: '-B',
103 clivalue: (params.fastp_B ?: '')
104 ],
105 'fastp_dedup': [
106 clihelp: 'Enable deduplication to drop the duplicated reads/pairs. ' +
107 "Default: ${params.fastp_dedup}",
108 cliflag: '--dedup',
109 clivalue: (params.fastp_dedup ? ' ' : '')
110 ],
111 'fastp_dup_calc_accuracy': [
112 clihelp: 'Accuracy level to calculate duplication (1~6), higher level uses more memory ' +
113 '(1G, 2G, 4G, 8G, 16G, 24G). Default 1 for no-dedup mode, and 3 for dedup mode. ' +
114 "Default: ${params.fastp_dup_calc_accuracy}",
115 cliflag: '--dup_calc_accuracy',
116 clivalue: (params.fastp_dup_calc_accuracy ?: '')
117 ],
118 'fastp_poly_g_min_len': [
119 clihelp: 'The minimum length to detect polyG in the read tail. ' +
120 "Default: ${params.fastp_poly_g_min_len}",
121 cliflag: '--poly_g_min_len',
122 clivalue: (params.fastp_poly_g_min_len ?: '')
123 ],
124 'fastp_G': [
125 clihelp: 'Disable polyG tail trimming. ' +
126 "Default: ${params.fastp_G}",
127 cliflag: '-G',
128 clivalue: (params.fastp_G ? ' ' : '')
129 ],
130 'fastp_x': [
131 clihelp: "Enable polyX trimming in 3' ends. " +
132 "Default: ${params.fastp_x}",
133 cliflag: 'x=',
134 clivalue: (params.fastp_x ? ' ' : '')
135 ],
136 'fastp_poly_x_min_len': [
137 clihelp: 'The minimum length to detect polyX in the read tail. ' +
138 "Default: ${params.fastp_poly_x_min_len}",
139 cliflag: '--poly_x_min_len',
140 clivalue: (params.fastp_poly_x_min_len ?: '')
141 ],
142 'fastp_cut_front': [
143 clihelp: "Move a sliding window from front (5') to tail, drop the bases in the window " +
144 'if its mean quality < threshold, stop otherwise. ' +
145 "Default: ${params.fastp_cut_front}",
146 cliflag: '--cut_front',
147 clivalue: (params.fastp_cut_front ? ' ' : '')
148 ],
149 'fastp_cut_tail': [
150 clihelp: "Move a sliding window from tail (3') to front, drop the bases in the window " +
151 'if its mean quality < threshold, stop otherwise. ' +
152 "Default: ${params.fastp_cut_tail}",
153 cliflag: '--cut_tail',
154 clivalue: (params.fastp_cut_tail ? ' ' : '')
155 ],
156 'fastp_cut_right': [
157 clihelp: "Move a sliding window from tail, drop the bases in the window and the right part " +
158 'if its mean quality < threshold, and then stop. ' +
159 "Default: ${params.fastp_cut_right}",
160 cliflag: '--cut_right',
161 clivalue: (params.fastp_cut_right ? ' ' : '')
162 ],
163 'fastp_W': [
164 clihelp: "Sliding window size shared by --fastp_cut_front, --fastp_cut_tail and " +
165 '--fastp_cut_right. ' +
166 "Default: ${params.fastp_W}",
167 cliflag: '--cut_window_size',
168 clivalue: (params.fastp_W ?: '')
169 ],
170 'fastp_M': [
171 clihelp: "The mean quality requirement shared by --fastp_cut_front, --fastp_cut_tail and " +
172 '--fastp_cut_right. ' +
173 "Default: ${params.fastp_M}",
174 cliflag: '--cut_mean_quality',
175 clivalue: (params.fastp_M ?: '')
176 ],
177 'fastp_q': [
178 clihelp: 'The quality value below which a base should is not qualified. ' +
179 "Default: ${params.fastp_q}",
180 cliflag: '-q',
181 clivalue: (params.fastp_q ?: '')
182 ],
183 'fastp_u': [
184 clihelp: 'What percent of bases are allowed to be unqualified. ' +
185 "Default: ${params.fastp_u}",
186 cliflag: '-u',
187 clivalue: (params.fastp_u ?: '')
188 ],
189 'fastp_n': [
190 clihelp: "How many N's can a read have. " +
191 "Default: ${params.fastp_n}",
192 cliflag: '-n',
193 clivalue: (params.fastp_n ?: '')
194 ],
195 'fastp_e': [
196 clihelp: "If the full reads' average quality is below this value, then it is discarded. " +
197 "Default: ${params.fastp_e}",
198 cliflag: '-e',
199 clivalue: (params.fastp_e ?: '')
200 ],
201 'fastp_l': [
202 clihelp: 'Reads shorter than this length will be discarded. ' +
203 "Default: ${params.fastp_l}",
204 cliflag: '-l',
205 clivalue: (params.fastp_l ?: '')
206 ],
207 'fastp_max_len': [
208 clihelp: 'Reads longer than this length will be discarded. ' +
209 "Default: ${params.fastp_max_len}",
210 cliflag: '--length_limit',
211 clivalue: (params.fastp_max_len ?: '')
212 ],
213 'fastp_y': [
214 clihelp: 'Enable low complexity filter. The complexity is defined as the percentage ' +
215 'of bases that are different from its next base (base[i] != base[i+1]). ' +
216 "Default: ${params.fastp_y}",
217 cliflag: '-y',
218 clivalue: (params.fastp_y ? ' ' : '')
219 ],
220 'fastp_Y': [
221 clihelp: 'The threshold for low complexity filter (0~100). Ex: A value of 30 means ' +
222 '30% complexity is required. ' +
223 "Default: ${params.fastp_Y}",
224 cliflag: '-Y',
225 clivalue: (params.fastp_Y ?: '')
226 ],
227 'fastp_U': [
228 clihelp: 'Enable Unique Molecular Identifier (UMI) pre-processing. ' +
229 "Default: ${params.fastp_U}",
230 cliflag: '-U',
231 clivalue: (params.fastp_U ? ' ' : '')
232 ],
233 'fastp_umi_loc': [
234 clihelp: 'Specify the location of UMI, can be one of ' +
235 'index1/index2/read1/read2/per_index/per_read. ' +
236 "Default: ${params.fastp_umi_loc}",
237 cliflag: '--umi_loc',
238 clivalue: (params.fastp_umi_loc ?: '')
239 ],
240 'fastp_umi_len': [
241 clihelp: 'If the UMI is in read1 or read2, its length should be provided. ' +
242 "Default: ${params.fastp_umi_len}",
243 cliflag: '--umi_len',
244 clivalue: (params.fastp_umi_len ?: '')
245 ],
246 'fastp_umi_prefix': [
247 clihelp: 'If specified, an underline will be used to connect prefix and UMI ' +
248 '(i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). ' +
249 "Default: ${params.fastp_umi_prefix}",
250 cliflag: '--umi_prefix',
251 clivalue: (params.fastp_umi_prefix ?: '')
252 ],
253 'fastp_umi_skip': [
254 clihelp: 'If the UMI is in read1 or read2, fastp can skip several bases following the UMI. ' +
255 "Default: ${params.fastp_umi_skip}",
256 cliflag: '--umi_skip',
257 clivalue: (params.fastp_umi_skip ?: '')
258 ],
259 'fastp_p': [
260 clihelp: 'Enable overrepresented sequence analysis. ' +
261 "Default: ${params.fastp_p}",
262 cliflag: '-p',
263 clivalue: (params.fastp_p ? ' ' : '')
264 ],
265 'fastp_P': [
266 clihelp: 'One in this many number of reads will be computed for overrepresentation analysis ' +
267 '(1~10000), smaller is slower. ' +
268 "Default: ${params.fastp_P}",
269 cliflag: '-P',
270 clivalue: (params.fastp_P ?: '')
271 ]
272 ]
273
274 toolspecs.each {
275 k, v -> tool.text['--' + k] = "${v.clihelp}"
276 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
277 }
278
279 return tool
280 }