DEMORT

00-scripts/demort.sh

+## 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

00-scripts/rename.sh

@@ -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" ]

01-infos/mullus_folders.txt

+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

main.sh

@@ -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