run_bwamem: 'Run BWA-mem job on farm'

In yangjl/maizeR: Generate pipelines for maize Genomic and Genetic analysis

Description

Fermikit is a de novo assembly based variant calling pipeline for Illumina short reads

Usage

run_bwamem(fq, kitpath = "/home/jolyang/bin/fermikit", s = "3g", t = 16,
  l = 100, arrayjobs = "1-2", jobid = "fermi", email = NULL)

Arguments

fq	An input data.frame for fastq files. Must contains fq1, fq2 and out.
kitpath	The absolute or relative path of the fermi.kit directory that can invoke the pipeline.
s	Approximate genome size, default=3g.
t	Number of threads, default=16.
l	Primary read length, default=100.
arrayjobs	A character specify the number of array you try to run, i.e. 1-100.
jobid	The job name show up in your sq NAME column.
email	Your email address that farm will email to once the job was done/failed.
genome	The full path of genome with bwa indexed reference fasta file.

Details

see more detail about fermikit by Li, Heng: https://github.com/lh3/fermikit

Value

return a batch of shell scripts.

Examples

fq <- data.frame(fq1=c("f_1.fq", "t_1.fq"), fq2=c("f_1.fq", "t_2.fq"), out=c("t1", "t2"))
run_fermikit(fq, kitpath="/home/jolyang/bin/fermikit/",
genome="/home/jolyang/dbcenter/AGP/AGPv2", s='3g', t=16, l=100, arrayjobs="1-2",
jobid="fermi", email=NULL)

yangjl/maizeR documentation built on May 4, 2019, 2:28 p.m.