one single command

main.sh

@@ -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 &