Commit 1af30749 authored by peguerin's avatar peguerin
Browse files

update command snakemake

parent 74a2ee39
......@@ -38,28 +38,28 @@ snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singul
cd ..
## demultiplex
cd 03_demultiplex
snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
cd ..
## filter samples
cd 04_filter_samples
snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
cd ..
## concatenate samples into run
for projet in `ls 04_filter_samples/04_filtered/`;
for projet in `ls results/04_filter_samples/04_filtered/`;
do
for marker in `ls 04_filter_samples/04_filtered/${projet}/`;
for marker in `ls results/04_filter_samples/04_filtered/${projet}/`;
do
for run in `ls 04_filter_samples/04_filtered/${projet}/${marker}/`;
for run in `ls results/04_filter_samples/04_filtered/${projet}/${marker}/`;
do
echo 04_filter_samples/04_filtered/${projet}/${marker}/${run};
mkdir -p 05_assignment/01_runs/${projet}/${marker}/
cat 04_filter_samples/04_filtered/${projet}/${marker}/${run}/*.c.r.l.u.fasta > 05_assignment/01_runs/${projet}/${marker}/${run}.fasta
echo results/04_filter_samples/04_filtered/${projet}/${marker}/${run};
mkdir -p results/05_assignment/01_runs/${projet}/${marker}/
cat results/04_filter_samples/04_filtered/${projet}/${marker}/${run}/*.c.r.l.u.fasta > results/05_assignment/01_runs/${projet}/${marker}/${run}.fasta
done
done
done
## assignment
cd 05_assignment
snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
cd ..
###############################################################################
......
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