DADA2_REMOVE_CHIMERAS

DADA2 Remove chimera sequences from the sequence table data using dada2 removeBimeraDenovo 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_remove_chimeras:
    input:
        "results/dada2/seqTab.RDS" # Sequence table
    output:
        "results/dada2/seqTab.nochim.RDS" # Chimera-free sequence table
    # 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/remove-chimeras/remove-chimeras.log"
    threads: 1 # set desired number of threads here
    wrapper:
        "0.72.0/bio/dada2/remove-chimeras"

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:

  • RDS file with the sequence table

Output:

  • RDS file with the chimera-free sequence table

Authors

  • Charlie Pauvert

Code

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

# Snakemake wrapper for removing chimeras sequences from
# the sequence table data using dada2 removeBimeraDenovo 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(
           unqs = readRDS(snakemake@input[[1]]),
           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::removeBimeraDenovo()")
}

# Remove chimeras
seqTab_nochimeras<-do.call(removeBimeraDenovo, args)

# Store the estimated errors as RDS files
saveRDS(seqTab_nochimeras, 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()