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#!/bin/bash -l
#PBS -N nfsmrnaseqsamplesheet
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=12:00:00

#work on current directory (folder)
cd $PBS_O_WORKDIR

#User defined variables
##########################################################
DIR='/path/to/raw/FASTQ/files'
INDEX='samplesheet.csv'
##########################################################

#load python module
module load python/3.10.8-gcccore-12.2.0

#fetch the script to create the sample metadata table
wget -L https://raw.githubusercontent.com/nf-core/rnaseq/master/bin/fastq_dir_to_samplesheet.py
chmod +x fastq_dir_to_samplesheet.py

#generate initial sample metadata file
./fastq_dir_to_samplesheet.py  $DIR index.csv \
        --strandedness auto \
        --read1_extension .fastq.gz

#format index file
cat index.csv | awk -F "," '{print $1 "," $2}' > ${INDEX}

#Remove intermediate files:
rm index.csv fastq_dir_to_samplesheet.py