#!/bin/bash

###########################################
# The CCseqBasic installation is located here :
pipePath="/t1-home/molhaem2/telenius/CCseqBasic/CS5/"
###########################################


# ___________________________________________
# The fastq files are located here (can be gzipped files, in that case remember to give --gz in the run command below)

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"


# ___________________________________________
# capturesiteFile is the RE fragment coordinate input file (containing the dpnII fragments within which your biotinylated capture oligos are) :
# Make this file with this tutorial : http://userweb.molbiol.ox.ac.uk/public/telenius/CaptureCompendium/CCseqBasic/3_run/fragmentfile.html

capturesiteFile="/t1-data/user/telenius/CCseqBasicFragmentFile.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"

# ___________________________________________
# This is the directory /REUSE_blat of a previous CCseqBasic run,
# probably ran with --onlyBlat flag , to speed up the actual analysis runs.
# To generate this folder, follow instructions in here : http://userweb.molbiol.ox.ac.uk/public/telenius/CaptureCompendium/CCseqBasic/3_run/onlyblat.html

# To not use this, leave the --BLATforREUSEfolderPath flag out of the command below
# or give '.' (i.e. "current directory") as the value of the flag (like below). 

# Example :
# reuseBLATdir="/t1-data/user/telenius/sample1/F4_blatPloidyFilteringLog_sample1_CS5/BlatPloidyFilterRun/REUSE_blat"

reuseBLATdir='.'


#############################################
# 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 CCseqBasic5.sh in folder ${rundir}"


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

echo "${pipePath}/CCseqBasic5.sh -c ${capturesiteFile} -s ${Sample} --pf ${PublicPath} --genome ${Genome} --chunkmb 1012 --R1 ${Read1} --R2 ${Read2} --BLATforREUSEfolderPath ${reuseBLATdir}"


# Run the command :

${pipePath}/CCseqBasic5.sh -c "${capturesiteFile}" -s "${Sample}" --pf "${PublicPath}" --genome ${Genome} --chunkmb 1012 --R1 ${Read1} --R2 ${Read2} --BLATforREUSEfolderPath ${reuseBLATdir}



# Tell the user that we are now finished :

echo "All done !"