runPipeline: Execute project workflow from FASTQ input to OTU output using...

In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses

Description

The analysis takes place in multiple steps beginning at the creation of a central output directory. Once the directory is created, a log-file is initilized that will contain all messages produced by DADA2. Accompanying the log file is a summary table documenting changes in read frequency following filtering and trimming procedures. This summary table can be used as a reference when determining the best way to modify different parameters input into the different functions.

Usage

runPipeline(
  configFile,
  isPaired = FALSE,
  getQuality = TRUE,
  getMergedSamples = TRUE,
  getDownloadedSeqs = FALSE,
  getTrimmedAdapters = FALSE
)

Arguments

configFile	Path to config file (YML-formatted).
isPaired	Default if FALSE. If TRUE workflow for paired end data is executed.
plotQuality	Default is TRUE. Sequence quality distribution is plotted using DADA2's plotQualityProfile method.
getMergeSamples	Default is TRUE. If FALSE, sample OTU tables will not be merged across.
downloadSeqs	Default is FALSE. If TRUE, users will be able to retrieve FASTQ files from SRA using the fastq2otu's getSeqs method.
trimAdapters	Default is FALSE. If TRUE, users will be able to remove adapters sequences from data using BBTools bbduk.sh script.

ananata/fastq2otu documentation built on Feb. 2, 2022, 4:20 p.m.