each snakemake step wait

main.sh

@@ -14,46 +14,46 @@
 ## * 2018-2020
 ##
 ##
-## Inspired by the Eric Coissac et al. obitools
-## Molecular Ecology Resources 2015
-##
 ## DESCRIPTION
 ## ===========
 ##
-## add sequences of gene from mitofish database
 ## 
 ##
 ##########################################################################
 CORES=$1
 CONFIGFILE=$2
 ##
-CORES=16
-CONFIGFILE="config/config_laperouse_marbec.yaml"
+#CORES=16
+#CONFIGFILE="config/config_laperouse_marbec.yaml"
 #CONFIGFILE="config/config_marbec_rapdirun_test.yaml"
 #CONFIGFILE="config/config_marbec_rapdirun_test_sdx.yaml"
 #CONFIGFILE="01_infos/config_test.yaml"
 #CONFIGFILE="01_infos/config_laperouse_alsace.yaml"
-
+#CONFIGFILE="config/config_tutorial_rapidrun.yaml"
 
 ###############################################################################
 ## write demultiplex table
 cd 01_settings
 snakemake --configfile "../"$CONFIGFILE -s readwrite_rapidrun_demultiplexing.py --cores $CORES
+wait
 cd ..
 ## assemble
 cd 02_assembly
 #snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
 snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
+wait
 cd ..
 ## demultiplex
 cd 03_demultiplex
 #snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
 snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
+wait
 cd ..
 ## filter samples
 cd 04_filter_samples
 #snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
 snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
+wait
 cd ..
 ## concatenate samples into run
 for projet in `ls results/04_filter_samples/04_filtered/`;
@@ -72,8 +72,9 @@ done
 cd 05_assignment
 #snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
 snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
+wait
 cd ..
-
+echo "proceeding rapidrun data with obitool...DONE."
 ############################################################################### 
 ## rename files
 # bash rename.sh 06_assignment