ln -s ../00-reads .
ln -s ../samples_id.txt .
echo "sample,fastq_1,fastq_2,strandedness" > samplesheet.csv
cat samples_id.txt | while read in; do echo "${in},00-reads/${in}_R1.fastq.gz,00-reads/${in}_R2.fastq.gz,reverse"; done >> samplesheet.csv

#module load Nextflow singularity

scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")

cat <<EOF > rnaseq.sbatch
#!/bin/sh
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 2
#SBATCH --mem 4G
#SBATCH --time 24:00:00
#SBATCH --partition middle_idx
#SBATCH --output $(date '+%Y%m%d')_rnaseq01.log
#SBATCH --chdir $scratch_dir

export NXF_OPTS="-Xms500M -Xmx4G"

/data/ucct/bi/pipelines/nf-core-rnaseq/nf-core-rnaseq-3.14.0/main.nf \\
          -c ../../DOC/hpc_slurm_rnaseq.config \\
          -params-file ../../DOC/hg38_ensmbl_rnaseq.yml \\
          --input samplesheet.csv \\
          --outdir 01-$(date '+%Y%m%d')_rnaseq \\
          --skip_markduplicates \\
          --pseudo_aligner salmon \\
          -resume
EOF

echo "sbatch rnaseq.sbatch" > _01_run_rnaseq.sh
