condor_sourcetracker: generates the condor file to performing quality control with...

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

Description

sourcetracker (Knights et al 2013, https://dx.doi.org/10.1038 fits a mixture model of the samples with sources as components, in our case we use the negative controls as such.

Usage

condor_sourcetracker(
  sourcetracker_asvfile = "",
  sourcetracker_negcontrol = "",
  sourcetracker_paramfile = "",
  sourcetracker_outdir = ".",
  top_asv = 50,
  max_split_size = 30,
  rarefaction_depth = NULL,
  sourcetracker_prefix = "sourcetracker",
  condor_file = "./condor_sourcetracker",
  batch_name = "sourcetracker_run",
  request_cores = 8,
  request_mem = "4 GB"
)

Arguments

sourcetracker_asvfile	name of the rds file with the asv matrix
sourcetracker_negcontrol	name of the rds file with the relationship between samples and negative controls
sourcetracker_paramfile	json file with sourcetracker's parameters
sourcetracker_outdir	directory where the results are saved
top_asv	number of ASVs to be used with sourcetracker to accelerate performance
max_split_size	max. number of samples to do by a cpu
rarefaction_depth	parameter to control for ASVs (OTUs) with higher abundance. This makes all taxa to have at most this abundance (by default NULL skips this step)
sourcetracker_prefix	prefix of the file with the results
condor_file	file where the condor commands are saved
batch_name	name of the batch
request_cores	Number of cpus to request by condor
request_mem	Memory request by condor

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