DADA2_MERGE_PAIRS

DADA2 Merging denoised forward and reverse reads using dada2 mergePairs 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_merge_pairs:
    input:
      dadaF="denoised/{sample}.1.RDS",# Inferred composition
      dadaR="denoised/{sample}.2.RDS",
      derepF="uniques/{sample}.1.RDS",# Dereplicated sequences
      derepR="uniques/{sample}.2.RDS"
    output:
        "merged/{sample}.RDS"
    # 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/merge-pairs/{sample}.log"
    threads: 1 # set desired number of threads here
    wrapper:
        "v3.8.0/bio/dada2/merge-pairs"

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=1.30.0

Input/Output

Input:

• dadaF: RDS file with the inferred sample composition from forward reads

• dadaR: reverse

• derepF: RDS file with the dereplicated forward reads

• derepR: reverse

Output:

• RDS file with the merged pairs

Params

• optional arguments for ``mergePairs(), 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 merging denoised forward and reverse reads using dada2 mergePairs 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(
           dadaF = snakemake@input[["dadaF"]],
           derepF = snakemake@input[["derepF"]],
           dadaR = snakemake@input[["dadaR"]],
           derepR = snakemake@input[["derepR"]]
           )
# Read RDS from the list
args<-sapply(args,readRDS)

# 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::mergePairs()")
}

# Merge pairs
merger<-do.call(mergePairs, args)

# Store the estimated errors as RDS files
saveRDS(merger, snakemake@output[[1]],compress = T)

# Close the connection for the log file
sink(type="message")
sink()