#!/bin/bash
#SBATCH --time 06:00:00
#SBATCH --mem 128G
#SBATCH --cpus-per-task 12

INPUT_DIR=/home/groups/ConradLab/rytis/data/FKBP6/run3/LIB220301DC
S1=LIB220301DC_M2350_S1_L004_R1_001.fastq.gz
S2=LIB220301DC_M2546_S3_L004_R1_001.fastq.gz
S3=LIB220301DC_M2548_S4_L004_R1_001.fastq.gz
S4=LIB220301DC_M2676_S2_L004_R1_001.fastq.gz

cd /home/groups/ConradLab/rytis/bin/COMPSRA

java -jar COMPSRA.jar \
 --ref_genome hg38 \
 --quality_control \
 --threads 12 \
 --project_name FKBP6 \
 --input ${INPUT_DIR}/${S1},${INPUT_DIR}/${S2},${INPUT_DIR}/${S3},${INPUT_DIR}/${S4} \
 --output FKBP6_run3 \
 --rm_adapter TGGAATTCTCGGGTGCCAAGG \
 --rm_bias 4 \
 --rm_low_quality_head 10 \
 --rm_low_quality_tail 10 \
 --rm_low_quality_read 10 \
 --rm_read_hard 16 \
 --alignment \
 --mapping_tool star \
 --mapping_reference hg38 \
 --annotation \
 --ann_class A1,A2,A3 \
 --ann_inCluster true \
 --ann_threshold 2