#module load R
#Fix pearl warning, add "export LC_ALL="en_US.UTF8" to .basrhc or run it now

mkdir logs

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

cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 32 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/ucct/bi/pipelines/flu-amd/flu-amd-1.2.0/IRMA FLU_AD ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} --external-config ../../../DOC/irma_config.sh &"; done > _01_irma_flu.sh

echo 'bash create_irma_stats_flu.sh' > _02_create_stats_flu.sh

echo 'bash postprocessing_flu.sh' > _03_post_processing_flu.sh

echo 'sed "s/__//g" irma_stats_flu.txt | sed "s/_\t/\t/g" > clean_irma_stats_flu.txt' >> _03_post_processing_flu.sh
