DADA2_ADD_SPECIES

DADA2 Adding species-level annotation using dada2 addSpecies function. Optional parameters are documented in the manual and the function is introduced in the dedicated tutorial section.

Example

This wrapper can be used in the following way:

rule dada2_add_species:
    input:
        taxtab="results/dada2/taxa.RDS", # Taxonomic assignments
        refFasta="resources/example_species_assignment.fa.gz" # Reference FASTA
    output:
        "results/dada2/taxa-sp.RDS", # Taxonomic + Species assignments
    # Even though this is an R wrapper, use named arguments in Python syntax
    # here, to specify extra parameters. Python booleans (`arg1=True`, `arg2=False`)
    # and lists (`list_arg=[]`) are automatically converted to R.
    # For a named list as an extra named argument, use a python dict
    #   (`named_list={name1=arg1}`).
    #params:
    #    verbose=True
    log:
        "logs/dada2/add-species/add-species.log"
    threads: 1 # set desired number of threads here
    wrapper:
        "0.72.0/bio/dada2/add-species"

Note that input, output and log file paths can be chosen freely. When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

  • bioconductor-dada2==1.16

Input/Output

Input:

  • taxa: RDS file containing the taxonomic assignments
  • refFasta: A string with the path to the FASTA reference database

Output:

  • The input RDS file augmented by the species-level annotation

Authors

  • Charlie Pauvert

Code

# __author__ = "Charlie Pauvert"
# __copyright__ = "Copyright 2020, Charlie Pauvert"
# __email__ = "cpauvert@protonmail.com"
# __license__ = "MIT"

# Snakemake wrapper for adding species-level
# annotation using dada2 assignTaxonomy function.

# Sink the stderr and stdout to the snakemake log file
# https://stackoverflow.com/a/48173272
log.file<-file(snakemake@log[[1]],open="wt")
sink(log.file)
sink(log.file,type="message")

library(dada2)

# Prepare arguments (no matter the order)
args<-list(
           taxtab = readRDS(snakemake@input[["taxtab"]]),
           refFasta = snakemake@input[["refFasta"]]
           )
# Check if extra params are passed
if(length(snakemake@params) > 0 ){
       # Keeping only the named elements of the list for do.call()
       extra<-snakemake@params[ names(snakemake@params) != "" ]
       # Add them to the list of arguments
       args<-c(args, extra)
} else{
    message("No optional parameters. Using default parameters from dada2::addSpecies()")
}

# Learn errors rates for both read types
taxa.sp<-do.call(addSpecies, args)

# Store the taxonomic assignments as a RDS file
saveRDS(taxa.sp, snakemake@output[[1]],compress = T)

# Proper syntax to close the connection for the log file
# but could be optional for Snakemake wrapper
sink(type="message")
sink()