Commit 0516c674 authored by peguerin's avatar peguerin
Browse files

add settings step

parent 2251d286
......@@ -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
......
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