metatran_LBE/20200728_quality_control_filtered.sh
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20200728_quality_control_filtered.sh
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			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 .