Commit 16aa114b authored by peguerin's avatar peguerin
Browse files

DEMORT

parent d55415e1
## species
#SPECIES=$1
SPECIES=mullus
## DEmultiplexing MOnitoring Report Tool
demort.py -t 16 -d 01-infos/"${SPECIES}"_folders.txt -o 98-metrics/"${SPECIES}"_samples.csv -p 98-metrics/"${SPECIES}"_samples.pdf
## 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
......@@ -2,9 +2,11 @@
## name of the file will be compatible with dDocent workflow
#argument 1 : path of the results 04-all_samples/species
#argument 2 : info files
#argument 3 : blacklist
mkdir -p 04-ddocent/$1
awk 'NR>1 { print $1"\t"$2"\t"$3"\t"$4}' $2 | while read LANE BARCODE POP SAMPLE ;
awk 'NR>1 { print $1"\t"$2"\t"$3"\t"$4}' $2 | grep -v -f <( awk -F, '{ print $1"\t"$2}' $3 | sed 's/sample_//g') | while read LANE BARCODE POP SAMPLE ;
do
FILE_SE=`ls $(pwd)/03-samples/$LANE | grep "sample_"$BARCODE".fq.gz"`
if [ -z "$FILE_SE" ]
......
03-samples/C6JATANXX_2
03-samples/C6JATANXX_3
03-samples/C6JATANXX_4
03-samples/C6JATANXX_5
03-samples/C6JATANXX_6
03-samples/C8BJGANXX_1
\ No newline at end of file
......@@ -16,8 +16,15 @@ snakemake -s 00-scripts/snakeFile.process_radtags -j 8 --use-singularity --confi
#rm -Rf 03-samples/* 10-logs/*
## DEmultiplexing MOnitoring Report Tool
bash 00-script/demort.sh "${SPECIES}"
## rename
bash 00-scripts/rename.sh "${SPECIES}" 01-infos/"${SPECIES}"_sample_information.csv
#### with blacklist
bash 00-scripts/rename.sh "${SPECIES}" 01-infos/"${SPECIES}"_sample_information.csv 98-metrics/"${SPECIES}"_samples_blacklist.txt
## dDocent
CONTAINER=/entrepot/working/seaconnect/seaConnect--dDocent/seaconnect.simg
......
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