add settings step

main.sh

@@ -22,15 +22,19 @@ CORES=$1
 CONFIGFILE=$2
 ##
 CORES=16
-CONFIGFILE="01_infos/config_test.yaml"
+CONFIGFILE="config/config_marbec_rapdirun_test.yaml"
+#CONFIGFILE="01_infos/config_test.yaml"
+#CONFIGFILE="01_infos/config_laperouse_alsace.yaml"
 
 
 ###############################################################################
 ## write demultiplex table
-snakemake --configfile $CONFIGFILE -s readwrite_rapidrun_demultiplexing.py
+cd 01_settings
+snakemake --configfile "../"$CONFIGFILE -s readwrite_rapidrun_demultiplexing.py --cores $CORES
+cd ..
 ## assemble
 cd 02_assembly
-snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
+snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
 cd ..
 ## demultiplex
 cd 03_demultiplex