condor_label_taxa: generate the input file to label taxa with condor

In welch16/microbiome.onglab: Wrapper functions to run dada2 with htCondor

Description

generate the input file to label taxa with condor

Usage

condor_label_taxa(
  asv_file = "",
  taxa_model_file = "",
  taxa_prefix = "taxa",
  taxa_outdir = ".",
  condor_file = "condor_label_taxa",
  batch_name = "dada2_label_taxa",
  confidence_thr = 60,
  request_cores = 4,
  request_mem = "4 GB"
)

Arguments

asv_file	rds file with the ASV table without chimeras
taxa_model_file	RData file with ta learned taxa model to use with DECIPHER
taxa_prefix	name of the output file
taxa_outdir	directory where the output is going to be saved
condor_file	name of the file with condor instructions
batch_name	string with the name of the batch
confidence_thr	confidence threshold, higher levels indicates higher accuracy
request_cores	number of cpus per machine
request_mem	number of GB required as memory

welch16/microbiome.onglab documentation built on March 12, 2020, 3:08 a.m.