Commit a9e2bdcc authored by peguerin's avatar peguerin
Browse files

DEMORT with singularity container

parent e4c2c943
## species
#SPECIES=$1
SPECIES=mullus
SPECIES=$1
CONTAINER=$2
## DEmultiplexing MOnitoring Report Tool
demort.py -t 16 -d 01-infos/"${SPECIES}"_folders.txt -o 98-metrics/"${SPECIES}"_samples.csv -p 98-metrics/"${SPECIES}"_samples.pdf
if [ -z "$CONTAINER" ]
then
## no singularity container
demort.py -t 16 -d 01-infos/"${SPECIES}"_folders.txt -o 98-metrics/"${SPECIES}"_samples.csv -p 98-metrics/"${SPECIES}"_samples.pdf
else
## use singularity container
singularity exec "${CONTAINER}" demort.py -t 16 -d 01-infos/"${SPECIES}"_folders.txt -o 98-metrics/"${SPECIES}"_samples.csv -p 98-metrics/"${SPECIES}"_samples.pdf
fi
## blacklisting individuals with low number of reads
awk -F, '$3+0 < 950500 {print $0}' 98-metrics/"${SPECIES}"_samples.csv > 98-metrics/"${SPECIES}"_samples_blacklist.txt
......@@ -26,7 +26,7 @@ snakemake -s 00-scripts/snakeFile.process_radtags -j 8 --use-singularity --confi
## DEmultiplexing MOnitoring Report Tool
bash 00-script/demort.sh "${SPECIES}"
bash 00-script/demort.sh "${SPECIES}" "${CONTAINER}"
## rename
#bash 00-scripts/rename.sh "${SPECIES}" 01-infos/"${SPECIES}"_sample_information.tsv
......
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