conda activate multiqc_env

export WORKING_DIR=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic
cd $WORKING_DIR

#Quality Control
##quality check on specific files
fastqc 31C_L1_R1_001_7JbTlroBLabe.fastq.gz 31C_L1_R2_001_yDmE80VNE4Et.fastq.gz 32C_L1_R1_001_wtOj7xHt2Rwh.fastq.gz 32C_L1_R2_001_wLqzFGxMmzNn.fastq.gz

##quality check on all fies ending by .fastq.gz
for filename in $(ls *'.fastq.gz')

do

fastqc $filename
done