DADA2_ASSIGN_TAXONOMY

DADA2 Classifying sequences against a reference database using dada2 assignTaxonomy function. Optional parameters are documented in the manual and the function is introduced in the dedicated tutorial section.

URL:

Example

This wrapper can be used in the following way:

rule dada2_assign_taxonomy:
    input:
        seqs="results/dada2/seqTab.nochim.RDS", # Chimera-free sequence table
        refFasta="resources/example_train_set.fa.gz" # Reference FASTA for taxonomy
    output:
        "results/dada2/taxa.RDS" # Taxonomic 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/assign-taxonomy/assign-taxonomy.log"
    threads: 1 # set desired number of threads here
    wrapper:
        "v1.1.0/bio/dada2/assign-taxonomy"

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:

  • seqs: RDS file with the chimera-free sequence table
  • refFasta: A string with the path to the FASTA reference database

Output:

  • RDS file containing the taxonomic assignments

Params

  • optional arguments for ``assignTaxonomy(), please provide them as python key=value pairs``:

Authors

  • Charlie Pauvert

Code

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

# Snakemake wrapper for classifying sequences against
# a reference database 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(
           seqs = readRDS(snakemake@input[["seqs"]]),
           refFasta = snakemake@input[["refFasta"]],
           multithread=snakemake@threads
           )
# 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::assignTaxonomy()")
}

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

# Store the taxonomic assignments as a RDS file
saveRDS(taxa, 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()