write_q2manifest: Generates a read manifest for importing sequencing data into...

In jbisanz/qiime2R: qiime2R

Generates a read manifest for importing sequencing data into qiime2

Description

Scans a directory for files with matching sequencing data (default: fastq.gz) and then generates a q2 compliant manifest.

Usage

write_q2manifest(outfile, directory, extension, paired, Fwd, Rev)

Arguments

outfile	filename for output (default: manifest_[timestamp].txt)
directory	directory containing reads
extension	file extension (default: .fastq.gz)
paired	are reads in paired format? TRUE/FALSE (default=FALSE)
Fwd	string used to denote a forward read (default= _R1)
Rev	string used to denote a reverse read (default= _R2)

Examples

## Not run: write_q2manifest("q2manifest.txt","/yourdirhere/reads/", extension=".fastq.gz", paired=TRUE)

jbisanz/qiime2R documentation built on April 24, 2024, 5 p.m.