conda activate multiqc_env

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

#Quality Control

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

do

fastqc $filename
done

#integrate fastqc reports
multiqc .