run_fq_dump: 'Run fastq-dump.'
In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

Description Usage Arguments Details Value Examples

fastq-dump to dump SRA file.

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run_fq_dump(inputdf, runnum = 100, dumppath, rmsra = FALSE,
  gzip = FALSE, email = NULL, slurmsh = "slurm-script/run_dump_",
  runinfo = c(FALSE, "bigmemh", 5, "5G", "16:00:00"))

`inputdf`	sra files in df as input. no need path info. [df, df["sra"]]
`runnum`	Number of running jobs in parallel. [int, =100]
`dumppath`	The absolute path of the SRA files to dump. [chr, "largedata/dump/"]
`rmsra`	Remove the original SRA file after dumpping. [logical, =TRUE]
`gzip`	GZIP the fastq files. [logical, =FALSE]
`email`	Your email address that farm will email to once the job was done/failed. [chr, "y@gmail.com"]
`slurmsh`	File name of the output shell command. [chr, ="slurm-script/run_dump_"]
`runinfo`	Parameters control the array job partition. A vector of c(TRUE, "bigmemh", "8196", "1"): 1) run or not, 2) -p partition name, 3) –mem, adn 4) –ntasks.

see more detail about SRA with Aspera downloading: http://www.ncbi.nlm.nih.gov/books/NBK158899/#SRA_download.downloading_sra_data_using

return a single shell script to run.

## run a single node job:
run_fq_dump(filepath="/group/jrigrp4/BS_teo20/WGBS",
            slurmsh="slurm-script/dump_WGBS.sh", rmsra=TRUE, email=NULL)

##  run array job:
run_fq_dump2(filepath="test", rmsra=TRUE, gzip=TRUE, email=NULL, run=c(TRUE, "bigmemh", "8196", "1"))