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1 # bettercallsal_db
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2
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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 `PDG000000002.3082`) 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`).
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4
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5 The `bettercallsal_db` workflow should finish within an hour with stable internet connection.
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6
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7 \
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8
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9
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10 ## Workflow Usage
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11
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12 ```bash
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13 cpipes --pipeline bettercallsal_db [options]
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14 ```
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15
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16 \
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17
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18
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19 Example: Run the `bettercallsal_db` pipeline and store output at `/data/Kranti_Konganti/bettercallsal_db/PDG000000002.3082`.
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20
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21 ```bash
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22 cpipes
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23 --pipeline bettercallsal_db \
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24 --pdg_release PDG000000002.3082 \
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25 --output /data/Kranti_Konganti/bettercallsal_db/PDG000000002.3082
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26 ```
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27
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28 \
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29
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30
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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.
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32
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33 ```bash
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34 cpipes
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35 --pipeline bettercallsal \
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36 --input /path/to/illumina/fastq/dir \
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37 --output /path/to/output \
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38 --bcs_root_dbdir /data/Kranti_Konganti/bettercallsal_db/PDG000000002.3082
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39 ```
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40
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41 \
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42
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43
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44 ## Note
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45
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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.
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47
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48 \
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49
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50
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51 ## `bettercallsal_db` CLI Help
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52
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53 ```text
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54 [Kranti_Konganti@my-unix-box ]$ cpipes --pipeline bettercallsal_db --help
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55
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56 N E X T F L O W ~ version 24.04.3
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57
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58 Launching `~/apps/bettercallsal/1.0.0/cpipes` [shrivelled_hamilton] DSL2 - revision: d9b4be42be
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59
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60 ================================================================================
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61 (o)
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62 ___ _ __ _ _ __ ___ ___
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63 / __|| '_ \ | || '_ \ / _ \/ __|
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64 | (__ | |_) || || |_) || __/\__ \
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65 \___|| .__/ |_|| .__/ \___||___/
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66 | | | |
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67 |_| |_|
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68 --------------------------------------------------------------------------------
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69 A collection of modular pipelines at CFSAN, FDA.
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70 --------------------------------------------------------------------------------
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71 Name : bettercallsal
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72 Author : Kranti Konganti
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73 Version : 0.9.0
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74 Center : CFSAN, FDA.
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75 ================================================================================
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76
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77 Workflow : bettercallsal_db
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78
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79 Author : Kranti Konganti
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80
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81 Version : 1.0.0
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82
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83
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84 Required :
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85
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86 --output : Absolute path to directory where all the
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87 pipeline outputs should be stored. Ex: --
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88 output /path/to/output
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89
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90 Other options :
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91
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92 --wcomp_serocol : Column number (non 0-based index) of the
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93 PDG metadata file by which the serotypes
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94 are collected. Default: false
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95
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96 --wcomp_seronamecol : Column number (non 0-based index) of the
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97 PDG metadata file whose column name is "
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98 serovar". Default: false
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99
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100 --wcomp_acc_col : Column number (non 0-based index) of the
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101 PDG metadata file whose column name is "acc
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102 ". Default: false
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103
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104 --wcomp_target_acc_col : Column number (non 0-based index) of the
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105 PDG metadata file whose column name is "
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106 target_acc". Default: false
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107
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108 --wcomp_complete_sero : Skip indexing serotypes when the serotype
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109 name in the column number 49 (non 0-based)
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110 of PDG metadata file consists a "-". For
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111 example, if an accession has a serotype=
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112 string as such in column number 49 (non 0-
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113 based): "serotype=- 13:z4,z23:-" then, the
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114 indexing of that accession is skipped.
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115 Default: false
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116
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117 --wcomp_not_null_serovar : Only index the computed_serotype column i.e
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118 . column number 49 (non 0-based), if the
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119 serovar column is not NULL. Default: false
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120
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121 --wcomp_i : Force include this serovar. Ignores --
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122 wcomp_complete_sero for only this serovar.
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123 Mention multiple serovars separated by a
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124 ! (Exclamation mark). Ex: --
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125 wcomp_complete_sero I 4,[5],12:i:-!Agona
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126 Default: false
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127
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128 --wcomp_num : Number of genome accessions to be collected
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129 per serotype. Default: false
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130
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131 --wcomp_min_contig_size : Minimum contig size to consider a genome
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132 for indexing. Default: false
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133
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134 --wsnp_serocol : Column number (non 0-based index) of the
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135 PDG metadata file by which the serotypes
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136 are collected. Default: false
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137
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138 --wsnp_seronamecol : Column number (non 0-based index) of the
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139 PDG metadata file whose column name is "
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140 serovar". Default: false
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141
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142 --wsnp_acc_col : Column number (non 0-based index) of the
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143 PDG metadata file whose column name is "acc
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144 ". Default: false
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145
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146 --wsnp_target_acc_col : Column number (non 0-based index) of the
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147 PDG metadata file whose column name is "
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148 target_acc". Default: false
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149
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150 --wsnp_complete_sero : Skip indexing serotypes when the serotype
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151 name in the column number 49 (non 0-based)
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152 of PDG metadata file consists a "-". For
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153 example, if an accession has a serotype=
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154 string as such in column number 49 (non 0-
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155 based): "serotype=- 13:z4,z23:-" then, the
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156 indexing of that accession is skipped.
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157 Default: true
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158
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159 --wsnp_not_null_serovar : Only index the computed_serotype column i.e
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160 . column number 49 (non 0-based), if the
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161 serovar column is not NULL. Default: false
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162
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163 --wsnp_i : Force include this serovar. Ignores --
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164 wsnp_complete_sero for only this serovar.
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165 Mention multiple serovars separated by a
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166 ! (Exclamation mark). Ex: --
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167 wsnp_complete_sero I 4,[5],12:i:-!Agona
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168 Default: 'I 4,[5],12:i
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169
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170 --wsnp_num : Number of genome accessions to collect per
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171 SNP cluster. Default: false
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172
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173 --mashsketch_run : Run `mash screen` tool. Default: true
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174
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175 --mashsketch_l : List input. Lines in each <input> specify
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176 paths to sequence files, one per line.
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177 Default: true
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178
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179 --mashsketch_I : <path> ID field for sketch of reads (
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180 instead of first sequence ID). Default:
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181 false
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182
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183 --mashsketch_C : <path> Comment for a sketch of reads (
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184 instead of first sequence comment). Default
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185 : false
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186
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187 --mashsketch_k : <int> K-mer size. Hashes will be based on
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188 strings of this many nucleotides.
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189 Canonical nucleotides are used by default (
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190 see Alphabet options below). (1-32) Default
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191 : 21
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192
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193 --mashsketch_s : <int> Sketch size. Each sketch will have
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194 at most this many non-redundant min-hashes
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195 . Default: 1000
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196
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197 --mashsketch_i : Sketch individual sequences, rather than
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198 whole files, e.g. for multi-fastas of
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199 single-chromosome genomes or pair-wise gene
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200 comparisons. Default: false
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201
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202 --mashsketch_S : <int> Seed to provide to the hash
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203 function. (0-4294967296) [42] Default:
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204 false
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205
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206 --mashsketch_w : <num> Probability threshold for warning
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207 about low k-mer size. (0-1) Default: false
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208
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209 --mashsketch_r : Input is a read set. See Reads options
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210 below. Incompatible with --mashsketch_i.
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211 Default: false
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212
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213 --mashsketch_b : <size> Use a Bloom filter of this size (
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214 raw bytes or with K/M/G/T) to filter out
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215 unique k-mers. This is useful if exact
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216 filtering with --mashsketch_m uses too much
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217 memory. However, some unique k-mers may
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218 pass erroneously, and copies cannot be
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219 counted beyond 2. Implies --mashsketch_r.
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220 Default: false
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221
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222 --mashsketch_m : <int> Minimum copies of each k-mer
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223 required to pass noise filter for reads.
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224 Implies --mashsketch_r. Default: false
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225
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226 --mashsketch_c : <num> Target coverage. Sketching will
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227 conclude if this coverage is reached before
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228 the end of the input file (estimated by
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229 average k-mer multiplicity). Implies --
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230 mashsketch_r. Default: false
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231
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232 --mashsketch_g : <size> Genome size (raw bases or with K/M/
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233 G/T). If specified, will be used for p-
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234 value calculation instead of an estimated
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235 size from k-mer content. Implies --
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236 mashsketch_r. Default: false
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237
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238 --mashsketch_n : Preserve strand (by default, strand is
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239 ignored by using canonical DNA k-mers,
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240 which are alphabetical minima of forward-
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241 reverse pairs). Implied if an alphabet is
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242 specified with --mashsketch_a or --
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243 mashsketch_z. Default: false
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244
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245 --mashsketch_a : Use amino acid alphabet (A-Z, except BJOUXZ
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246 ). Implies --mashsketch_n --mashsketch_k 9
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247 . Default: false
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248
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249 --mashsketch_z : <text> Alphabet to base hashes on (case
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250 ignored by default; see --mashsketch_Z). K-
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251 mers with other characters will be ignored
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252 . Implies --mashsketch_n. Default: false
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253
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254 --mashsketch_Z : Preserve case in k-mers and alphabet (case
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255 is ignored by default). Sequence letters
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256 whose case is not in the current alphabet
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257 will be skipped when sketching. Default:
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258 false
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259
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260 Help options :
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261
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262 --help : Display this message.
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263
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264 ```
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