Commit bc770038 authored by peguerin's avatar peguerin

control quality bash

parent 0b9be3c4
## perform a fastqc
## singularity container path with fastqc
SINGULARITY_IMG="/media/superdisk/utils/conteneurs/recettes/fastqc.simg"
## folder with fastq files path
RUN_FOLDER="/media/superdisk/popedna/donnees/ngs/mullus_surmuletus/"
for FICHIER in $(ls ${RUN_FOLDER})
do
SAMPLE=`basename ${FICHIER}`
singularity run --bind /media/superdisk:/media/superdisk/ $SINGULARITY_IMG ${RUN_FOLDER}/${SAMPLE}.fastq.gz -o mullus_surmuletus/fastqc_report/
done
## cluster fastqc report
#docker run -v ${RUN_FOLDER}:${RUN_FOLDER} -w ${RUN_FOLDER} ewels/multiqc
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