Commit 34141842 authored by peguerin's avatar peguerin
Browse files

each snakemake step wait

parent 1bd96edf
......@@ -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
......
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