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1 # bettercallsal_db
2
3 `bettercallsal_db` is an end-to-end automated workflow to generate and consolidate the required DB flat files based on [NCBI Pathogens Database for Salmonella](https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/). It first downloads the metadata based on the provided release identifier (Ex: `latest_snps` or `PDG000000002.2876`) and then creates a `mash sketch` based on the filtering strategy. It generates two types of sketches, one that prioritizes genome collection based on SNP clustering (`per_snp_cluster`) and the other just collects up to N number of genome accessions for each `computed_serotype` column from the metadata file (`per_computed_serotype`).
4
5 The `bettercallsal_db` workflow should finish within an hour with stable internet connection.
6
7 \
8  
9
10 ## Workflow Usage
11
12 ```bash
13 cpipes --pipeline bettercallsal_db [options]
14 ```
15
16 \
17  
18
19 Example: Run the `bettercallsal_db` pipeline and store output at `/data/Kranti_Konganti/bettercallsal_db/PDG000000002.2876`.
20
21 ```bash
22 cpipes
23 --pipeline bettercallsal_db \
24 --pdg_release PDG000000002.2876 \
25 --output /data/Kranti_Konganti/bettercallsal_db/PDG000000002.2876
26 ```
27
28 \
29  
30
31 Now you can run the `bettercallsal` workflow with the created database by mentioning the root path to the database with `--bcs_root_dbdir` option.
32
33 ```bash
34 cpipes
35 --pipeline bettercallsal \
36 --input /path/to/illumina/fastq/dir \
37 --output /path/to/output \
38 --bcs_root_dbdir /data/Kranti_Konganti/bettercallsal_db/PDG000000002.2876
39 ```
40
41 \
42  
43
44 ## Note
45
46 Please note that the last step of the `bettercallsal_db` workflow named `SCAFFOLD_GENOMES` will spawn multiple processes and is not cached by **Nextflow**. This is an intentional setup for this specific stage of the workflow to speed up database creation and as such it is recommended that you run this workflow in a grid computing or similar cloud computing setting.
47
48 \
49  
50
51 ## `bettercallsal_db` CLI Help
52
53 ```text
54 [Kranti_Konganti@my-unix-box ]$ cpipes --pipeline bettercallsal_db --help
55 N E X T F L O W ~ version 23.04.3
56 Launching `./bettercallsal/cpipes` [special_brenner] DSL2 - revision: 8da4e11078
57 ================================================================================
58 (o)
59 ___ _ __ _ _ __ ___ ___
60 / __|| '_ \ | || '_ \ / _ \/ __|
61 | (__ | |_) || || |_) || __/\__ \
62 \___|| .__/ |_|| .__/ \___||___/
63 | | | |
64 |_| |_|
65 --------------------------------------------------------------------------------
66 A collection of modular pipelines at CFSAN, FDA.
67 --------------------------------------------------------------------------------
68 Name : bettercallsal
69 Author : Kranti Konganti
70 Version : 0.7.0
71 Center : CFSAN, FDA.
72 ================================================================================
73
74 Workflow : bettercallsal_db
75
76 Author : Kranti Konganti
77
78 Version : 0.7.0
79
80
81 Required :
82
83 --output : Absolute path to directory where all the
84 pipeline outputs should be stored. Ex: --
85 output /path/to/output
86
87 Other options :
88
89 --wcomp_serocol : Column number (non 0-based index) of the
90 PDG metadata file by which the serotypes
91 are collected. Default: false
92
93 --wcomp_seronamecol : Column number (non 0-based index) of the
94 PDG metadata file whose column name is "
95 serovar". Default: false
96
97 --wcomp_acc_col : Column number (non 0-based index) of the
98 PDG metadata file whose column name is "acc
99 ". Default: false
100
101 --wcomp_target_acc_col : Column number (non 0-based index) of the
102 PDG metadata file whose column name is "
103 target_acc". Default: false
104
105 --wcomp_complete_sero : Skip indexing serotypes when the serotype
106 name in the column number 49 (non 0-based)
107 of PDG metadata file consists a "-". For
108 example, if an accession has a serotype=
109 string as such in column number 49 (non 0-
110 based): "serotype=- 13:z4,z23:-" then, the
111 indexing of that accession is skipped.
112 Default: false
113
114 --wcomp_not_null_serovar : Only index the computed_serotype column i.e
115 . column number 49 (non 0-based), if the
116 serovar column is not NULL. Default: false
117
118 --wcomp_i : Force include this serovar. Ignores --
119 wcomp_complete_sero for only this serovar.
120 Mention multiple serovars separated by a
121 ! (Exclamation mark). Ex: --
122 wcomp_complete_sero I 4,[5],12:i:-!Agona
123 Default: false
124
125 --wcomp_num : Number of genome accessions to be collected
126 per serotype. Default: false
127
128 --wcomp_min_contig_size : Minimum contig size to consider a genome
129 for indexing. Default: false
130
131 --wsnp_serocol : Column number (non 0-based index) of the
132 PDG metadata file by which the serotypes
133 are collected. Default: false
134
135 --wsnp_seronamecol : Column number (non 0-based index) of the
136 PDG metadata file whose column name is "
137 serovar". Default: false
138
139 --wsnp_acc_col : Column number (non 0-based index) of the
140 PDG metadata file whose column name is "acc
141 ". Default: false
142
143 --wsnp_target_acc_col : Column number (non 0-based index) of the
144 PDG metadata file whose column name is "
145 target_acc". Default: false
146
147 --wsnp_complete_sero : Skip indexing serotypes when the serotype
148 name in the column number 49 (non 0-based)
149 of PDG metadata file consists a "-". For
150 example, if an accession has a serotype=
151 string as such in column number 49 (non 0-
152 based): "serotype=- 13:z4,z23:-" then, the
153 indexing of that accession is skipped.
154 Default: true
155
156 --wsnp_not_null_serovar : Only index the computed_serotype column i.e
157 . column number 49 (non 0-based), if the
158 serovar column is not NULL. Default: false
159
160 --wsnp_i : Force include this serovar. Ignores --
161 wsnp_complete_sero for only this serovar.
162 Mention multiple serovars separated by a
163 ! (Exclamation mark). Ex: --
164 wsnp_complete_sero I 4,[5],12:i:-!Agona
165 Default: 'I 4,[5],12:i
166
167 --wsnp_num : Number of genome accessions to collect per
168 SNP cluster. Default: false
169
170 --mashsketch_run : Run `mash screen` tool. Default: true
171
172 --mashsketch_l : List input. Lines in each <input> specify
173 paths to sequence files, one per line.
174 Default: true
175
176 --mashsketch_I : <path> ID field for sketch of reads (
177 instead of first sequence ID). Default:
178 false
179
180 --mashsketch_C : <path> Comment for a sketch of reads (
181 instead of first sequence comment). Default
182 : false
183
184 --mashsketch_k : <int> K-mer size. Hashes will be based on
185 strings of this many nucleotides.
186 Canonical nucleotides are used by default (
187 see Alphabet options below). (1-32) Default
188 : 21
189
190 --mashsketch_s : <int> Sketch size. Each sketch will have
191 at most this many non-redundant min-hashes
192 . Default: 1000
193
194 --mashsketch_i : Sketch individual sequences, rather than
195 whole files, e.g. for multi-fastas of
196 single-chromosome genomes or pair-wise gene
197 comparisons. Default: false
198
199 --mashsketch_S : <int> Seed to provide to the hash
200 function. (0-4294967296) [42] Default:
201 false
202
203 --mashsketch_w : <num> Probability threshold for warning
204 about low k-mer size. (0-1) Default: false
205
206 --mashsketch_r : Input is a read set. See Reads options
207 below. Incompatible with --mashsketch_i.
208 Default: false
209
210 --mashsketch_b : <size> Use a Bloom filter of this size (
211 raw bytes or with K/M/G/T) to filter out
212 unique k-mers. This is useful if exact
213 filtering with --mashsketch_m uses too much
214 memory. However, some unique k-mers may
215 pass erroneously, and copies cannot be
216 counted beyond 2. Implies --mashsketch_r.
217 Default: false
218
219 --mashsketch_m : <int> Minimum copies of each k-mer
220 required to pass noise filter for reads.
221 Implies --mashsketch_r. Default: false
222
223 --mashsketch_c : <num> Target coverage. Sketching will
224 conclude if this coverage is reached before
225 the end of the input file (estimated by
226 average k-mer multiplicity). Implies --
227 mashsketch_r. Default: false
228
229 --mashsketch_g : <size> Genome size (raw bases or with K/M/
230 G/T). If specified, will be used for p-
231 value calculation instead of an estimated
232 size from k-mer content. Implies --
233 mashsketch_r. Default: false
234
235 --mashsketch_n : Preserve strand (by default, strand is
236 ignored by using canonical DNA k-mers,
237 which are alphabetical minima of forward-
238 reverse pairs). Implied if an alphabet is
239 specified with --mashsketch_a or --
240 mashsketch_z. Default: false
241
242 --mashsketch_a : Use amino acid alphabet (A-Z, except BJOUXZ
243 ). Implies --mashsketch_n --mashsketch_k 9
244 . Default: false
245
246 --mashsketch_z : <text> Alphabet to base hashes on (case
247 ignored by default; see --mashsketch_Z). K-
248 mers with other characters will be ignored
249 . Implies --mashsketch_n. Default: false
250
251 --mashsketch_Z : Preserve case in k-mers and alphabet (case
252 is ignored by default). Sequence letters
253 whose case is not in the current alphabet
254 will be skipped when sketching. Default:
255 false
256
257 Help options :
258
259 --help : Display this message.
260
261 ```