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snakemake_only_obitools
snakemake_only_obitools
Commit 69f6d531 authored by peguerin's avatar peguerin
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change name folder

parent c92db63c
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Showing with 5 additions and 4 deletions
clean.sh
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## 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
View file @ 69f6d531
......@@ -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
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