Commit cfc6059e authored by peguerin's avatar peguerin
Browse files

one single command

parent 901b9f5e
......@@ -37,54 +37,11 @@ CONFIGFILE=$2
#CONFIGFILE="config/config_tutorial_rapidrun.yaml"
#CONFIGFILE="config/config_tutorial_classic.yaml"
###############################################################################
## write demultiplex table
cd 01_settings
snakemake --configfile "../"$CONFIGFILE -s readwrite_rapidrun_demultiplexing.py --cores $CORES
wait
cd ..
## assemble
cd 02_assembly
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
wait
cd ..
## demultiplex
cd 03_demultiplex
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
wait
cd ..
## filter samples
cd 04_filter_samples
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
wait
cd ..
## concatenate samples into run
for projet in `ls results/04_filter_samples/04_filtered/`;
do
for marker in `ls results/04_filter_samples/04_filtered/${projet}/`;
do
for run in `ls results/04_filter_samples/04_filtered/${projet}/${marker}/`;
do
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 --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
wait
cd ..
echo "DONE"
#rm -rf results;mkdir results;snakemake --configfile config/config_test_rapidrun.yaml --cores 8 --use-conda
snakemake --configfile $CONFIGFILE --cores $CORES --use-conda
###############################################################################
## rename files
# bash rename.sh 06_assignment
## clean
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --delete-all-output --dry-run
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --delete-all-output --rerun-incomplete --cores 8
#nohup snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20 &
......
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