condor_merge_pairs: generate the input to filter and trim the fastq files with...

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

Description

generate the input to filter and trim the fastq files with condor

Usage

condor_merge_pairs(
  merge_queue_file = "",
  merge_param_file = "",
  merge_outdir = ".",
  error_rate_files = c("R1.rds", "R2.rds"),
  condor_file = "./condor_merge_pairs",
  batch_name = "dada2_merge_pairs",
  request_cores = 4,
  request_mem = "4 GB"
)

Arguments

merge_queue_file	name of the file with the queue, it has 3 columns sample_name | R1.fastq | R2.fastq
merge_param_file	name of the file with the merge pairs parameters
merge_outdir	directory where the output is going to be saved
error_rate_files	vector with names of the learned error rates
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.