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

format main script

parent 9e800eed
......@@ -13,49 +13,41 @@
###############################################################################
## Usage:
## CORE=16
## bash main.sh $CORES
## CONFIGFILE=path/to/my/configfile.yaml
## bash main.sh $CORES $CONFIGFILE
##
##
###############################################################################
CORES=$1
CONFIGFILE=$2
##
CORES=32
CONFIGFILE="../01_infos/config_test.yaml"
###############################################################################
## write demultiplex table
snakemake --configfile 01_infos/config_test.yaml -s readwrite_rapidrun_demultiplexing.py
## assemble
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 ..
## demultiplex
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
cd ..
## quality files
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 ..
## cluster
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 ..
###############################################################################
## clean
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 --dry-run
#snakemake --configfile $CONFIGFILE -s Snakefile --delete-all-output --rerun-incomplete
rm -Rf 04_quality/*
\ No newline at end of file
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