prep_gbs.sge

#!/bin/bash

#prep_gbs.sge
#sge submission script to run qc pipeline on raw sequencing reads
#M. Supple
#last modified 1 July 2015

#usage
#qsub prep_gbs.sge <prep.input>
#<prep.input>:  see prep.example.input or example at end of this script

#requires
#axe
#trimmit
#load_lane.sh

#output
#filtered interleaved fastq file for each sample
#various qc reports



#$ -N prep_gbs
#$ -o prep_gbs.output
#$ -pe threads 11
#$ -l virtual_free=1.8g,h_vmem=1.9g
#$ -cwd
#$ -j y



#print some sge info
echo Job $JOB_NAME started `date` in queue $QUEUE with id=$JOB_ID on `hostname`

#read the input file
source $1

#run the demultiplex and cleaning pipeline
bash /borevitz/gbs/code/load_lane.sh  $threads $user $lane_name $barcode_file $file1 $file2

#print note that job completed
echo done `date`


##example input file for qc and prepping reads
#
##input fastq files
#file1=/PATH/TO/FASTQ/FILE/sample_R1_001.fastq.gz
#file2=/PATH/TO/FASTQ/FILE/sample_R2_001.fastq.gz
#
##sequencing and sample information
#lane_name=LANE_NAME
#barcode_file=LANE_BARCODES.tab
#
##user group for output
#user=Eucalyptus
#
##number of threads to use
#threads=11