Commit 69f6d531 authored by peguerin's avatar peguerin
Browse files

change name folder

parent c92db63c

clean.sh

+1 −1
Original line number Diff line number Diff line 
## remove all files generated by this workflow

rm -Rf assembled log 
 No newline at end of file
 
rm -Rf 01-assembly 99-log 02-demultiplex
 
 No newline at end of file

main.sh

+4 −3
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ FOLDER_INPUT=$1 
REFERENCE_BASE=$2

CORES=$3

# working folders

mkdir -p assembled barcodes raw log samples runs tables

mkdir -p 01-assembly 02-demultiplex 99-log runs tables

# link base reference

ln -s $REFERENCE_BASE bdr

# link raw sequences data
@@ -22,8 +22,9 @@ snakemake -s scripts/step2.sf -j $CORES --latency-wait 120 
snakemake -s scripts/step3.sf -j $CORES --latency-wait 120

snakemake -s scripts/step4.sf -j $CORES --latency-wait 120



## this work !



snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk"

mkdir -p 01-assembly 02-demultiplex 99-log 

snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120



rm -Rf assembled log 
 No newline at end of file