conda activate multiqc_env

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

#Quality Control

##quality check on all files after SortMeRNA on non-aligned sequences
for filename in $(ls *'non_aligned.fastq')

do

fastqc $filename
done

#integrate fastqc reports
multiqc .