run_fermikit: 'Run Fermikit 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_fermikit(fq, kitpath = "$HOME/bin/fermikit", ref.fa = "", s = "2.3g",
  l = 100, email = NULL, runinfo = c(FALSE, "bigmemh", 1))

run_fermikit_vcfcall(bamdir = "", kitpath = "$HOME/bin/fermikit",
  ref.fa = "", email = NULL, runinfo = c(FALSE, "bigmemh", 1))

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.
ref.fa	The full path of genome with bwa indexed reference fasta file.
s	Approximate genome size, default=2.3g.
l	Primary read length, default=100.
email	Your email address that farm will email to once the job was done/failed.
runinfo	Parameters specify the array job partition information. A vector of c(FALSE, "bigmemh", "1"): 1) run or not, default=FALSE 2) -p partition name, default=bigmemh and 3) –cpus, default=1. It will pass to set_array_job.
bamdir	Path of the bam files.

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/",
             ref.fa="path/to/fastq.fa", s='2.3g', l=100,
             email=NULL, runinfo = c(FALSE, "bigmemh", 1)

run_fermikit(bamdir="", kitpath="$HOME/bin/fermikit",
             ref.fa="",
             email=NULL, runinfo = c(FALSE, "bigmemh", 1))

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