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+# bettercallsal_db
+
+`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 `PDG000000002.2537`) 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`).
+
+The `bettercallsal_db` workflow should finish within an hour with stable internet connection.
+
+\
+ 
+
+## Workflow Usage
+
+```bash
+cpipes --pipeline bettercallsal_db [options]
+```
+
+\
+ 
+
+Example: Run the `bettercallsal_db` pipeline and store output at `/data/Kranti_Konganti/bettercallsal_db`.
+
+```bash
+cpipes
+      --pipeline bettercallsal_db \
+      --pdg_release PDG000000002.2537 \
+      --output /data/Kranti_Konganti/bettercallsal_db
+```
+
+\
+ 
+
+Now you can run the `bettercallsal` workflow with the created database by mentioning the root path to the database with `--bcs_root_dbdir` option.
+
+```bash
+cpipes
+      --pipeline bettercallsal \
+      --input /path/to/illumina/fastq/dir \
+      --output /path/to/output \
+      --bcs_root_dbdir /data/Kranti_Konganti/bettercallsal_db
+```
+
+\
+ 
+
+## Note
+
+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.
+
+\
+ 
+
+## `bettercallsal_db` CLI Help
+
+```text
+[Kranti_Konganti@my-unix-box ]$ cpipes --pipeline bettercallsal_db --help
+N E X T F L O W  ~  version 22.10.0
+Launching `./bettercallsal/cpipes` [hopeful_franklin] DSL2 - revision: 93f5293f50
+================================================================================
+             (o)
+  ___  _ __   _  _ __    ___  ___
+ / __|| '_ \ | || '_ \  / _ \/ __|
+| (__ | |_) || || |_) ||  __/\__ \
+ \___|| .__/ |_|| .__/  \___||___/
+      | |       | |
+      |_|       |_|
+--------------------------------------------------------------------------------
+A collection of modular pipelines at CFSAN, FDA.
+--------------------------------------------------------------------------------
+Name                            : CPIPES
+Author                          : Kranti Konganti
+Version                         : 0.5.0
+Center                          : CFSAN, FDA.
+================================================================================
+
+Workflow                        : bettercallsal_db
+
+Author                          : Kranti Konganti
+
+Version                         : 0.4.0
+
+
+Required                        :
+
+--output                        : Absolute path to directory where all the
+                                  pipeline outputs should be stored. Ex: --
+                                  output /path/to/output
+
+Other options                   :
+
+--wcomp_serocol                 : Column number (non 0-based index) of the
+                                  PDG metadata file by which the serotypes
+                                  are collected. Default: false
+
+--wcomp_complete_sero           : Skip indexing serotypes when the serotype
+                                  name in the column number 49 (non 0-based)
+                                  of PDG metadata file consists a "-". For
+                                  example, if an accession has a serotype=
+                                  string as such in column number 49 (non 0-
+                                  based): "serotype=- 13:z4,z23:-" then, the
+                                  indexing of that accession is skipped.
+                                  Default: false
+
+--wcomp_not_null_serovar        : Only index the computed_serotype column i.e
+                                  . column number 49 (non 0-based), if the
+                                  serovar column is not NULL.  Default: false
+
+--wcomp_i                       : Force include this serovar. Ignores --
+                                  wcomp_complete_sero for only this serovar.
+                                  Mention multiple serovars separated by a
+                                  ! (Exclamation mark). Ex: --
+                                  wcomp_complete_sero I 4,[5],12:i:-!Agona
+                                  Default: false
+
+--wcomp_num                     : Number of genome accessions to be collected
+                                  per serotype. Default: false
+
+--wcomp_min_contig_size         : Minimum contig size to consider a genome
+                                  for indexing. Default: false
+
+--wsnp_serocol                  : Column number (non 0-based index) of the
+                                  PDG metadata file by which the serotypes
+                                  are collected. Default: false
+
+--wsnp_complete_sero            : Skip indexing serotypes when the serotype
+                                  name in the column number 49 (non 0-based)
+                                  of PDG metadata file consists a "-". For
+                                  example, if an accession has a serotype=
+                                  string as such in column number 49 (non 0-
+                                  based): "serotype=- 13:z4,z23:-" then, the
+                                  indexing of that accession is skipped.
+                                  Default: true
+
+--wsnp_not_null_serovar         : Only index the computed_serotype column i.e
+                                  . column number 49 (non 0-based), if the
+                                  serovar column is not NULL.  Default: false
+
+--wsnp_i                        : Force include this serovar. Ignores --
+                                  wsnp_complete_sero for only this serovar.
+                                  Mention multiple serovars separated by a
+                                  ! (Exclamation mark). Ex: --
+                                  wsnp_complete_sero I 4,[5],12:i:-!Agona
+                                  Default: 'I 4,[5],12:i
+
+--wsnp_num                      : Number of genome accessions to collect per
+                                  SNP cluster. Default: false
+
+--mashsketch_run                : Run `mash screen` tool. Default: true
+
+--mashsketch_l                  : List input. Lines in each <input> specify
+                                  paths to sequence files, one per line.
+                                  Default: true
+
+--mashsketch_I                  : <path>  ID field for sketch of reads (
+                                  instead of first sequence ID). Default:
+                                  false
+
+--mashsketch_C                  : <path>  Comment for a sketch of reads (
+                                  instead of first sequence comment). Default
+                                  : false
+
+--mashsketch_k                  : <int>   K-mer size. Hashes will be based on
+                                  strings of this many nucleotides.
+                                  Canonical nucleotides are used by default (
+                                  see Alphabet options below). (1-32) Default
+                                  : 21
+
+--mashsketch_s                  : <int>   Sketch size. Each sketch will have
+                                  at most this many non-redundant min-hashes
+                                  . Default: 1000
+
+--mashsketch_i                  : Sketch individual sequences, rather than
+                                  whole files, e.g. for multi-fastas of
+                                  single-chromosome genomes or pair-wise gene
+                                  comparisons. Default: false
+
+--mashsketch_S                  : <int>   Seed to provide to the hash
+                                  function. (0-4294967296) [42] Default:
+                                  false
+
+--mashsketch_w                  : <num>   Probability threshold for warning
+                                  about low k-mer size. (0-1) Default: false
+
+--mashsketch_r                  : Input is a read set. See Reads options
+                                  below. Incompatible with --mashsketch_i.
+                                  Default: false
+
+--mashsketch_b                  : <size>  Use a Bloom filter of this size (
+                                  raw bytes or with K/M/G/T) to filter out
+                                  unique k-mers. This is useful if exact
+                                  filtering with --mashsketch_m uses too much
+                                  memory. However, some unique k-mers may
+                                  pass erroneously, and copies cannot be
+                                  counted beyond 2. Implies --mashsketch_r.
+                                  Default: false
+
+--mashsketch_m                  : <int>   Minimum copies of each k-mer
+                                  required to pass noise filter for reads.
+                                  Implies --mashsketch_r. Default: false
+
+--mashsketch_c                  : <num>   Target coverage. Sketching will
+                                  conclude if this coverage is reached before
+                                  the end of the input file (estimated by
+                                  average k-mer multiplicity). Implies --
+                                  mashsketch_r. Default: false
+
+--mashsketch_g                  : <size>  Genome size (raw bases or with K/M/
+                                  G/T). If specified, will be used for p-
+                                  value calculation instead of an estimated
+                                  size from k-mer content. Implies --
+                                  mashsketch_r. Default: false
+
+--mashsketch_n                  : Preserve strand (by default, strand is
+                                  ignored by using canonical DNA k-mers,
+                                  which are alphabetical minima of forward-
+                                  reverse pairs). Implied if an alphabet is
+                                  specified with --mashsketch_a or --
+                                  mashsketch_z. Default: false
+
+--mashsketch_a                  : Use amino acid alphabet (A-Z, except BJOUXZ
+                                  ). Implies --mashsketch_n --mashsketch_k 9
+                                  . Default: false
+
+--mashsketch_z                  : <text>  Alphabet to base hashes on (case
+                                  ignored by default; see --mashsketch_Z). K-
+                                  mers with other characters will be ignored
+                                  . Implies --mashsketch_n. Default: false
+
+--mashsketch_Z                  : Preserve case in k-mers and alphabet (case
+                                  is ignored by default). Sequence letters
+                                  whose case is not in the current alphabet
+                                  will be skipped when sketching. Default:
+                                  false
+
+Help options                    :
+
+--help                          : Display this message.
+
+```