condor_filter_trim: generate the input to filter and trim the fastq files with...
In welch16/microbiome.onglab: Wrapper functions to run dada2 with htCondor

View source: R/filter_and_trim_functions.R

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

condor_filter_trim(
  trim_queue_file = "",
  trim_param_file = "",
  trim_outdir = ".",
  condor_file = "./condor_filter_trim",
  batch_name = "dada2_trim_sequences",
  request_cores = 4,
  request_mem = "4 GB"
)

`trim_queue_file`	name of the file with the queue, it has 3 columns sample_name \| R1.fastq \| R2.fastq
`trim_param_file`	name of the file with the filter and trim parameters
`trim_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