format main script

main.sh

@@ -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