## Generate the samples list
# go to the Data directory
cd ../Data
# subtitute "_L00" and any following character by nothing
ls Raw_Data | sed 's/_L00.*//' | uniq > samples.txt

## Generate the paths to the fastq files divided by samples
# make directory to hold the lists
mkdir -p fastq_lists

# for each sample
while read -r sample
do
    # extract the fastq names from that sample and separate the lanes by comas
    ls -d $(pwd)/Raw_Data/* |  grep $sample | grep R1 | sed -z 's/\n/,/g;s/,$/\n/' \
    > fastq_lists/${sample}_R1.csv
    
    ls -d $(pwd)/Raw_Data/* | grep $sample | grep R2 | sed -z 's/\n/,/g;s/,$/\n/' \
    > fastq_lists/${sample}_R2.csv
    
    # create a single file with both R1 and R2 (separate by space)
#    paste -d " " fastq_lists/${sample}_R2.csv  fastq_lists/${sample}_R1.csv \
#    > fastq_lists/${sample}.csv
    
    # tidy up removing the intermediate files
#     rm fastq_lists/*{R1,R2}.csv
     
 done < samples.txt