set -o pipefail | set -o pipefail | ||||
set -e | set -e | ||||
pigz -p 8 -dc ${fastq1} > ${sample_id}_R1.fastq | |||||
pigz -p 8 -dc ${fastq2} > ${sample_id}_R2.fastq | |||||
pigz -p 16 -dc ${fastq1} > ${sample_id}_R1.fastq | |||||
pigz -p 16 -dc ${fastq2} > ${sample_id}_R2.fastq | |||||
STAR \ | STAR \ | ||||
--runThreadN 8 \ | --runThreadN 8 \ | ||||
--genomeDir ${STAR_INDEX_DIR} \ | --genomeDir ${STAR_INDEX_DIR} \ |