condor_remove_chimeras: generate the input file to remove chimeras from the sequence...

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

Description

generate the input file to remove chimeras from the sequence table with condor

Usage

condor_remove_chimeras(
  sequence_table_file = "",
  chim_param_file = "",
  chim_prefix = "remove_chimeras",
  chim_outdir = ".",
  condor_file = "./condor_remove_chimeras",
  batch_name = "dada2_remove_chimeras",
  request_cores = 4,
  request_mem = "4 GB"
)

Arguments

sequence_table_file	name of the file with the sequence tables to merge (one p/line)
chim_param_file	name of the remove chimeras parameter file
chim_prefix	prefix name for the sequence table output file
chim_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
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.