Commit 22a20c30 authored by peguerin's avatar peguerin
Browse files

format main script

parent 9e800eed
...@@ -13,49 +13,41 @@ ...@@ -13,49 +13,41 @@
############################################################################### ###############################################################################
## Usage: ## Usage:
## CORE=16 ## CORE=16
## bash main.sh $CORES ## CONFIGFILE=path/to/my/configfile.yaml
## bash main.sh $CORES $CONFIGFILE
## ##
## ##
############################################################################### ###############################################################################
CORES=$1 CORES=$1
CONFIGFILE=$2 CONFIGFILE=$2
##
CORES=32 CORES=32
CONFIGFILE="../01_infos/config_test.yaml" CONFIGFILE="../01_infos/config_test.yaml"
############################################################################### ###############################################################################
## write demultiplex table ## write demultiplex table
snakemake --configfile 01_infos/config_test.yaml -s readwrite_rapidrun_demultiplexing.py snakemake --configfile 01_infos/config_test.yaml -s readwrite_rapidrun_demultiplexing.py
## assemble ## assemble
cd 02_assembly cd 02_assembly
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120 snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
cd .. cd ..
## demultiplex ## demultiplex
cd 03_demultiplexing cd 03_demultiplexing
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20 --dry-run
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20 snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
cd .. cd ..
## quality files ## quality files
cd 04_cat_quality cd 04_cat_quality
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20 --dry-run snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
cd .. cd ..
## cluster ## cluster
cd 05_clustering cd 05_clustering
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20 --dry-run snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
cd .. cd ..
############################################################################### ###############################################################################
## clean ## clean
snakemake --configfile $CONFIGFILE -s Snakefile --delete-all-output --dry-run #snakemake --configfile $CONFIGFILE -s Snakefile --delete-all-output --dry-run
snakemake --configfile $CONFIGFILE -s Snakefile --delete-all-output --rerun-incomplete #snakemake --configfile $CONFIGFILE -s Snakefile --delete-all-output --rerun-incomplete
rm -Rf 04_quality/*
\ No newline at end of file
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