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.
URL:
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:
"0.80.1/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 assignmentsrefFasta
: A string with the path to the FASTA reference database
Output:
- The input RDS file augmented by the species-level annotation
Params¶
optional arguments for ``addSpecies()
, please provide them as pythonkey=value
pairs``:
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()