#!/bin/bash


# =============================================================================================================================================================
# ==                                                          SLURM parameters                                                                               ==
# =============================================================================================================================================================

#SBATCH --nodes=1   
#SBATCH --ntasks-per-node=2
#SBATCH --mem=8GB
#SBATCH --time=24:00:00
#SBATCH --job-name=ReadCount
#SBATCH --output=slurm-Anne-%j.log


# =============================================================================================================================================================
# ==                                                          Load modules                                                                               ==
# =============================================================================================================================================================

module load FastQC/0.11.9-Java-11
cpu=2

# =============================================================================================================================================================
# ==                                                          Functions                                                                               ==
# =============================================================================================================================================================

function my_fastq_readcount {
 name=$1
 fastq=$2
 echo $name $(zgrep -c "^+$" $datadir/$fastq) >> $resultsdir/00.fastq.counts
}

function my_fastqc {
 # NOTE: not used in this script
 name=$1
 fastq=$2
 printf "\n========== FastQC: "$name" ======================================\n" 
 my_mkdir $resultsdir/$name
 fastqc -t $cpu -o $resultsdir/$name -f fastq $datadir/$fastq
}

function my_mkdir {
 if [ ! -d $1 ]; then
  mkdir $1 ;
 fi
}


# =============================================================================================================================================================
# ==                                                          Main script                                                                               ==
# =============================================================================================================================================================


datadir=/scratch/p127804/PROJECTS/PrimBio/20240113/fastq
resultsdir=/scratch/p127804/PROJECTS/PrimBio/20240113/readcounts
my_mkdir $resultsdir

# below you see: 1) function, 2) name of the sample and 3) the fastq filename

	
# my_fastq_readcount Bd01 Bd1_6321_S84_R1_001.fastq.gz
# my_fastq_readcount Cm01 Cm1_6282_S45_R1_001.fastq.gz
# my_fastq_readcount Cm02 Cm2_6283_S46_R1_001.fastq.gz
# my_fastq_readcount Cm03 Cm3_6284_S47_R1_001.fastq.gz
# my_fastq_readcount Cm04 Cm4_6285_S48_R1_001.fastq.gz
# my_fastq_readcount Cm05 Cm5_6286_S49_R1_001.fastq.gz
# my_fastq_readcount Cm06 Cm6_6287_S50_R1_001.fastq.gz
# my_fastq_readcount Cm07 Cm7_6288_S51_R1_001.fastq.gz
# my_fastq_readcount Cm08 Cm8_6289_S52_R1_001.fastq.gz
# my_fastq_readcount Cm09 Cm9_6290_S53_R1_001.fastq.gz
# my_fastq_readcount Cm10 Cm10_6291_S54_R1_001.fastq.gz
# my_fastq_readcount Cm11 Cm11_6292_S55_R1_001.fastq.gz
# my_fastq_readcount Cm12 Cm12_6293_S56_R1_001.fastq.gz
# my_fastq_readcount Cm13 Cm13_6294_S57_R1_001.fastq.gz
# my_fastq_readcount Cm14 Cm14_6295_S58_R1_001.fastq.gz
# my_fastq_readcount Cm15 Cm15_6296_S59_R1_001.fastq.gz
# my_fastq_readcount Cm16 Cm16_6297_S60_R1_001.fastq.gz
# my_fastq_readcount Cm17 Cm17_6298_S61_R1_001.fastq.gz
# my_fastq_readcount Cm18 Cm18_6299_S62_R1_001.fastq.gz
# my_fastq_readcount Cm19 Cm19_6300_S63_R1_001.fastq.gz
# my_fastq_readcount Cm20 Cm20_6301_S64_R1_001.fastq.gz
# my_fastq_readcount Cm21 Cm21_6302_S65_R1_001.fastq.gz
# my_fastq_readcount Cm22 Cm22_6303_S66_R1_001.fastq.gz
# my_fastq_readcount Cm23 Cm23_6304_S67_R1_001.fastq.gz
# my_fastq_readcount Dg01 Dg1_6278_S41_R1_001.fastq.gz
# my_fastq_readcount Dg02 Dg2_6279_S42_R1_001.fastq.gz
# my_fastq_readcount Dg03 Dg3_6280_S43_R1_001.fastq.gz
# my_fastq_readcount Dg04 Dg4_6281_S44_R1_001.fastq.gz
# my_fastq_readcount Fx01 Fx1_6316_S79_R1_001.fastq.gz
# my_fastq_readcount Fx02 Fx2_6317_S80_R1_001.fastq.gz
# my_fastq_readcount Po01 Po1_6305_S68_R1_001.fastq.gz
# my_fastq_readcount Po02 Po2_6306_S69_R1_001.fastq.gz
# my_fastq_readcount Po03 Po3_6307_S70_R1_001.fastq.gz
# my_fastq_readcount Po04 Po4_6308_S71_R1_001.fastq.gz
# my_fastq_readcount Po05 Po5_6309_S72_R1_001.fastq.gz
# my_fastq_readcount Po06 Po6_6310_S73_R1_001.fastq.gz
# my_fastq_readcount Po07 Po7_6311_S74_R1_001.fastq.gz
# my_fastq_readcount Po08 Po8_6312_S75_R1_001.fastq.gz
# my_fastq_readcount Po09 Po9_6313_S76_R1_001.fastq.gz
# my_fastq_readcount Po10 Po10_6314_S77_R1_001.fastq.gz
# my_fastq_readcount Po11 Po11_6315_S78_R1_001.fastq.gz
# my_fastq_readcount Ra01 Ra1_6238_S1_R1_001.fastq.gz
# my_fastq_readcount Ra02 Ra2_6239_S2_R1_001.fastq.gz
# my_fastq_readcount Ra03 Ra3_6240_S3_R1_001.fastq.gz
# my_fastq_readcount Ra04 Ra4_6241_S4_R1_001.fastq.gz
# my_fastq_readcount Ra05 Ra5_6242_S5_R1_001.fastq.gz
# my_fastq_readcount Ra06 Ra6_6243_S6_R1_001.fastq.gz
# my_fastq_readcount Ra07 Ra7_6244_S7_R1_001.fastq.gz
# my_fastq_readcount Ra08 Ra8_6245_S8_R1_001.fastq.gz
# my_fastq_readcount Ra09 Ra9_6246_S9_R1_001.fastq.gz
# my_fastq_readcount Ra10 Ra10_6247_S10_R1_001.fastq.gz
# my_fastq_readcount Ra11 Ra11_6248_S11_R1_001.fastq.gz
# my_fastq_readcount Ra12 Ra12_6249_S12_R1_001.fastq.gz
# my_fastq_readcount Ra13 Ra13_6250_S13_R1_001.fastq.gz
# my_fastq_readcount Ra14 Ra14_6251_S14_R1_001.fastq.gz
# my_fastq_readcount Ra15 Ra15_6252_S15_R1_001.fastq.gz
# my_fastq_readcount Ra16 Ra16_6253_S16_R1_001.fastq.gz
# my_fastq_readcount Ra17 Ra17_6254_S17_R1_001.fastq.gz
# my_fastq_readcount Ra18 Ra18_6255_S18_R1_001.fastq.gz
# my_fastq_readcount Ra19 Ra19_6256_S19_R1_001.fastq.gz
# my_fastq_readcount Ra20 Ra20_6257_S20_R1_001.fastq.gz
# my_fastq_readcount Ra21 Ra21_6258_S21_R1_001.fastq.gz
# my_fastq_readcount Ra22 Ra22_6259_S22_R1_001.fastq.gz
# my_fastq_readcount Ra23 Ra23_6260_S23_R1_001.fastq.gz
# my_fastq_readcount Ra24 Ra24_6261_S24_R1_001.fastq.gz
# my_fastq_readcount Ra25 Ra25_6262_S25_R1_001.fastq.gz
# my_fastq_readcount Ra26 Ra26_6263_S26_R1_001.fastq.gz
# my_fastq_readcount Ra27 Ra27_6264_S27_R1_001.fastq.gz
# my_fastq_readcount Ra28 Ra28_6265_S28_R1_001.fastq.gz
# my_fastq_readcount Ra29 Ra29_6266_S29_R1_001.fastq.gz
# my_fastq_readcount Ra30 Ra30_6267_S30_R1_001.fastq.gz
# my_fastq_readcount Ra31 Ra31_6268_S31_R1_001.fastq.gz
# my_fastq_readcount Ra32 Ra32_6269_S32_R1_001.fastq.gz
# my_fastq_readcount Ra33 Ra33_6270_S33_R1_001.fastq.gz
# my_fastq_readcount Ra34 Ra34_6271_S34_R1_001.fastq.gz
# my_fastq_readcount Ra35 Ra35_6272_S35_R1_001.fastq.gz
# my_fastq_readcount Ra36 Ra36_6273_S36_R1_001.fastq.gz
# my_fastq_readcount Ra37 Ra37_6274_S37_R1_001.fastq.gz
# my_fastq_readcount Ra38 Ra38_6275_S38_R1_001.fastq.gz
# my_fastq_readcount Ra39 Ra39_6276_S39_R1_001.fastq.gz
# my_fastq_readcount Ra40 Ra40_6277_S40_R1_001.fastq.gz
# my_fastq_readcount Sk01 Sk1_6318_S81_R1_001.fastq.gz
# my_fastq_readcount Sk02 Sk2_6319_S82_R1_001.fastq.gz
# my_fastq_readcount Sk03 Sk3_6320_S83_R1_001.fastq.gz
# my_fastq_readcount Wc01 Wc1_6322_S85_R1_001.fastq.gz
# my_fastq_readcount Wc02 Wc2_6323_S86_R1_001.fastq.gz
# my_fastq_readcount Wc03 Wc3_6324_S87_R1_001.fastq.gz
# my_fastq_readcount Wc04 Wc4_6325_S88_R1_001.fastq.gz
# my_fastq_readcount Wc05 Wc5_6326_S89_R1_001.fastq.gz
# my_fastq_readcount Wc06 Wc6_6327_S90_R1_001.fastq.gz


datadir=/scratch/p127804/PROJECTS/PrimBio/20240113/sortmerna
resultsdir=/scratch/p127804/PROJECTS/PrimBio/20240113/readcounts_sortmerna
my_mkdir $resultsdir

# my_fastq_readcount Bd01 Bd01_fwd.fq.gz 
# my_fastq_readcount Cm01 Cm01_fwd.fq.gz 
# my_fastq_readcount Cm02 Cm02_fwd.fq.gz 
# my_fastq_readcount Cm03 Cm03_fwd.fq.gz 
# my_fastq_readcount Cm04 Cm04_fwd.fq.gz 
# my_fastq_readcount Cm05 Cm05_fwd.fq.gz 
# my_fastq_readcount Cm06 Cm06_fwd.fq.gz 
# my_fastq_readcount Cm07 Cm07_fwd.fq.gz 
# my_fastq_readcount Cm08 Cm08_fwd.fq.gz 
# my_fastq_readcount Cm09 Cm09_fwd.fq.gz 
# my_fastq_readcount Cm10 Cm10_fwd.fq.gz 
# my_fastq_readcount Cm11 Cm11_fwd.fq.gz 
# my_fastq_readcount Cm12 Cm12_fwd.fq.gz 
# my_fastq_readcount Cm13 Cm13_fwd.fq.gz 
# my_fastq_readcount Cm14 Cm14_fwd.fq.gz 
# my_fastq_readcount Cm15 Cm15_fwd.fq.gz 
# my_fastq_readcount Cm16 Cm16_fwd.fq.gz 
# my_fastq_readcount Cm17 Cm17_fwd.fq.gz 
# my_fastq_readcount Cm18 Cm18_fwd.fq.gz 
# my_fastq_readcount Cm19 Cm19_fwd.fq.gz 
# my_fastq_readcount Cm20 Cm20_fwd.fq.gz 
# my_fastq_readcount Cm21 Cm21_fwd.fq.gz 
# my_fastq_readcount Cm22 Cm22_fwd.fq.gz 
# my_fastq_readcount Cm23 Cm23_fwd.fq.gz 
# my_fastq_readcount Dg01 Dg01_fwd.fq.gz 
# my_fastq_readcount Dg02 Dg02_fwd.fq.gz 
# my_fastq_readcount Dg03 Dg03_fwd.fq.gz 
# my_fastq_readcount Dg04 Dg04_fwd.fq.gz 
# my_fastq_readcount Fx01 Fx01_fwd.fq.gz 
# my_fastq_readcount Fx02 Fx02_fwd.fq.gz 
# my_fastq_readcount Po01 Po01_fwd.fq.gz 
# my_fastq_readcount Po02 Po02_fwd.fq.gz 
# my_fastq_readcount Po03 Po03_fwd.fq.gz 
# my_fastq_readcount Po04 Po04_fwd.fq.gz 
# my_fastq_readcount Po05 Po05_fwd.fq.gz 
# my_fastq_readcount Po06 Po06_fwd.fq.gz 
# my_fastq_readcount Po07 Po07_fwd.fq.gz 
# my_fastq_readcount Po08 Po08_fwd.fq.gz 
# my_fastq_readcount Po09 Po09_fwd.fq.gz 
# my_fastq_readcount Po10 Po10_fwd.fq.gz 
# my_fastq_readcount Po11 Po11_fwd.fq.gz 
# my_fastq_readcount Ra01 Ra01_fwd.fq.gz 
# my_fastq_readcount Ra02 Ra02_fwd.fq.gz 
# my_fastq_readcount Ra03 Ra03_fwd.fq.gz 
# my_fastq_readcount Ra04 Ra04_fwd.fq.gz 
# my_fastq_readcount Ra05 Ra05_fwd.fq.gz 
# my_fastq_readcount Ra06 Ra06_fwd.fq.gz 
# my_fastq_readcount Ra07 Ra07_fwd.fq.gz 
# my_fastq_readcount Ra08 Ra08_fwd.fq.gz 
# my_fastq_readcount Ra09 Ra09_fwd.fq.gz 
# my_fastq_readcount Ra10 Ra10_fwd.fq.gz 
# my_fastq_readcount Ra11 Ra11_fwd.fq.gz 
# my_fastq_readcount Ra12 Ra12_fwd.fq.gz 
# my_fastq_readcount Ra13 Ra13_fwd.fq.gz 
# my_fastq_readcount Ra14 Ra14_fwd.fq.gz 
# my_fastq_readcount Ra15 Ra15_fwd.fq.gz 
# my_fastq_readcount Ra16 Ra16_fwd.fq.gz 
# my_fastq_readcount Ra17 Ra17_fwd.fq.gz 
# my_fastq_readcount Ra18 Ra18_fwd.fq.gz 
# my_fastq_readcount Ra19 Ra19_fwd.fq.gz 
# my_fastq_readcount Ra20 Ra20_fwd.fq.gz 
# my_fastq_readcount Ra21 Ra21_fwd.fq.gz 
# my_fastq_readcount Ra22 Ra22_fwd.fq.gz 
# my_fastq_readcount Ra23 Ra23_fwd.fq.gz 
# my_fastq_readcount Ra24 Ra24_fwd.fq.gz 
# my_fastq_readcount Ra25 Ra25_fwd.fq.gz 
# my_fastq_readcount Ra26 Ra26_fwd.fq.gz 
# my_fastq_readcount Ra27 Ra27_fwd.fq.gz 
# my_fastq_readcount Ra28 Ra28_fwd.fq.gz 
# my_fastq_readcount Ra29 Ra29_fwd.fq.gz 
# my_fastq_readcount Ra30 Ra30_fwd.fq.gz 
# my_fastq_readcount Ra31 Ra31_fwd.fq.gz 
# my_fastq_readcount Ra32 Ra32_fwd.fq.gz 
# my_fastq_readcount Ra33 Ra33_fwd.fq.gz 
# my_fastq_readcount Ra34 Ra34_fwd.fq.gz 
# my_fastq_readcount Ra35 Ra35_fwd.fq.gz 
# my_fastq_readcount Ra36 Ra36_fwd.fq.gz 
# my_fastq_readcount Ra37 Ra37_fwd.fq.gz 
# my_fastq_readcount Ra38 Ra38_fwd.fq.gz 
# my_fastq_readcount Ra39 Ra39_fwd.fq.gz 
# my_fastq_readcount Ra40 Ra40_fwd.fq.gz 
# my_fastq_readcount Sk01 Sk01_fwd.fq.gz 
# my_fastq_readcount Sk02 Sk02_fwd.fq.gz 
# my_fastq_readcount Sk03 Sk03_fwd.fq.gz 
# my_fastq_readcount Wc01 Wc01_fwd.fq.gz 
# my_fastq_readcount Wc02 Wc02_fwd.fq.gz 
# my_fastq_readcount Wc03 Wc03_fwd.fq.gz 
# my_fastq_readcount Wc04 Wc04_fwd.fq.gz 
# my_fastq_readcount Wc05 Wc05_fwd.fq.gz 
# my_fastq_readcount Wc06 Wc06_fwd.fq.gz