run_GBSv2: 'Run TASSEL GBSv2 on slurm-based HPC'
In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

a single slurm job. help doc: https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline

run_GBSv2(outdir = "largedata/gbs", shfile, fqdir, keyfile, bt2_idx, sam,
  ref, snpqc_file, h5, db = NULL, mem, cpu, kmerlen = 64,
  enzyme = "ApeKI", mnlcov = 0.05, mnmaf = 0.01,
  deleteolddata = "true", production = FALSE, seq2tag = TRUE,
  tag2fq = TRUE, bt2 = TRUE, snpcall = TRUE)

GBSSeqToTag(shfile, mem, fqdir, db, keyfile, kmerlen, enzyme)

TagExportToFastq(shfile, mem, db, tagexport, mindepth = 1)

run_bowtie2(shfile, cpu, bt2_idx, tagexport, sam)

SAMToGBSdb(shfile, mem, sam, db)

DiscoverySNP(shfile, mem, db, ref, mnlcov = 0.05, mnmaf = 0.001,
  deleteolddata)

SNPQuality(shfile, mem, db, snpqc_file)

ProductionSNPCaller(shfile, mem, db, enzyme, fqdir, keyfile, kmerlen, h5)

`shfile`	A shell script in "slurm-script/". [chr, "slurm-script/run_it.sh"]
`fqdir`	Absolute dir for the fastq files, can be nested within the dir. [chr, "my/fq/filedir"]
`keyfile`	The key file. The GBSv2 key file has 4 required headers: Flowcell, Lane, Barcode and FullSampleName. [chr, "data/file.txt]
`bt2_idx`	The idx file for bowtie2. [chr, "/lustre/work/jyanglab/jyang21/dbcenter/AGP/AGPv4/AGPv4_bt2_index/AGPv4_bt2_index"]
`sam`	The output sam file. [chr, "tagexport/tagsForAlignFullvs_F1s.sam"]
`ref`	Fastq file of the ref. [chr, "/lustre/work/jyanglab/jyang21/dbcenter/AGP/AGPv4/AGPv4_bt2_index/AGPv4_bt2.fa"]
`snpqc_file`	SNP qc file. [chr, "largedata/gbs/outputStats.txt"]
`h5`	Output hdf5 format. [chr, "gbs/discovery/output.h5"]
`db`	Relative file name of the db. [chr, =NULL, or "data/gbs.db"]
`mem`	Memory usage. [num, 50]
`cpu`	Number of CPUs to use. [num, 50]
`kmerlen`	Kmer length [num, =64]
`enzyme`	Enzyme used for cutting. [chr, ="ApeKI"]
`mnlcov`	mnLCov. [num, =0.05]
`mnmaf`	Min MAF. [num, =0.001]
`deleteolddata`	Delete Old Data. [chr, ="true"]
`production`	SNP production. [logical, =F]
`seq2tag`	Generated tags from fastq files. [logical, =T]
`tag2fq`	extract tags from db for alignment to reference. [logical, =T]
`bt2`	Run bt2 alignment. [logical, =T]
`snpcall`	Call SNP. [logical, =T]
`tagexport`	Fastq.gz file to export tags. [chr, "tagexport/tagsForAlign.fa.gz"]
`mindepth`	The minimum count of reads for a tag to be output. [num, =1]