run_cutadapt: 'Run cutadapt'

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

Description

install in .local/bin using 'pip install –user –upgrade cutadapt'.

Usage

run_cutadapt(inputdf, ad1 = "AGATCGGAAGAGC", ad2 = "AGATCGGAAGAGC",
  q = 20, email = NULL, runinfo = c(FALSE, "bigmemh", 1))

Arguments

inputdf	Data.frame with fq1, fq2, out1, out2, and report columns. Both input and output can be gzipped (.gz).
ad1	Adapter 3' method, see cutadapt documentation for more details. Same for ad2.
q	quality_cutoff Default=20. Note:use -q0 to get the distribution of all quality values
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.

Details

For more information: https://cutadapt.readthedocs.io/en/stable/index.html version: v1.10

Value

return A batch of shell scripts.

Examples

fqs <- c("$HOME/dbcenter/Ecoli/fastq/SRR2921970.sra_1.fastq.gz",
         "$HOME/dbcenter/Ecoli/fastq/SRR2921970.sra_2.fastq.gz")
inputdf <- data.frame(fq1=fqs[1], fq2=fqs[2], out1=fqs[1], out2=fqs[2])
run_cutadapt(inputdf, ad1="AGATCGGAAGAGC", ad2="AGATCGGAAGAGC", q=20,
             email=NULL, runinfo = c(FALSE, "bigmemh", 1))

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