#!/bin/bash

###########################################
# The pipeline is located here :
pipePath="/t1-data/data/hugheslab/jelenatools/CCseqBasic/CS5"
###########################################


# The fastq files are located here (these cannot be .gz packed files)

Read1="/t1-data/user/telenius/R1_001.fastq"
Read2="/t1-data/user/telenius/R2_001.fastq"

# This is the genome build for the run :

Genome="hg19"


# This is the oligo coordinate input file (containing the dpnII fragments within which your biotinylated capture oligos are) :
# Make this file with this tutorial : http://sara.molbiol.ox.ac.uk/public/telenius/captureManual/Generating_Oligo_Coordinate_File_For_CaptureC_analyser.pdf

OligoFile="/t1-data/user/telenius/oligoDpnFragments.txt"


# This is the path to the public folder we want to put the data into (this folder can exist, but it does not need to) :

PublicPath="/public/telenius/CAPTUREC_DATA/sample_run4_data"

# This is the name we give our sample (no fancy characters, don't start the name with a number)

Sample="sample_run4"

CCstyle="CS5"
# Select duplicate filtering style :
# CS3 : CC3 style (good for short sequencing reads)
# CS4 : CC4 style (good for long sequencing reads)
# CS5 : CC5 style (in between CC3 and CC4 - good for all reads)


#############################################
# We are now here (the current directory) - the directory we are now running the pipe :

rundir=$( pwd )


# Tell where we are - print it to output :

echo "Running pipe.sh in folder ${rundir}"


# Tell the command to user - print it to output :

echo "${pipePath}/pipe.sh -o "${OligoFile}" -s "${Sample}" --pf "${PublicPath}" --genome ${Genome} --chunkmb 1012 --R1 ${Read1} --R2 ${Read2} --CCversion ${CCstyle}"


# Run the command :

${pipePath}/pipe.sh -o "${OligoFile}" -s "${Sample}" --pf "${PublicPath}" --genome ${Genome} --chunkmb 1012 --R1 ${Read1} --R2 ${Read2} --CCversion ${CCstyle}



# Tell the user that we are now finished :

echo "All done !"