create_sample_sheet: Creates a sample sheet file names in the provided folder

In flow-r/ngsflows: Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr

Description

This function would check for files ending in fastq.gz, fq.gz, fastq, fq.

Usage

create_sample_sheet(path, project, subproject, runid, format,
  fix.names = FALSE, fix.names.char = "-", out_sep = c("\t", ","),
  include.undetermined = FALSE, pattern = "fastq.gz|fq.gz|fastq|fq",
  outfile)

Arguments

path	path to the fastq files
project	name of the project. optional
subproject	name of the subproject optional
runid	name of the flowcell this data is from optional
format	the format for names of fastq files, we have defaults for CASAVA and miSeq
fix.names	change the sample names such that they are acceptable as column names for R
pattern	extensions this function will look for optional
outfile	name of the output csv files optional

Examples

## Not run: 
create_sample_mat(levelipath)

## End(Not run)

flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.