main snakemake command

main.sh

-# arguments
-FOLDER_INPUT=$1
-REFERENCE_BASE=$2
-CORES=$3
-# working folders
-mkdir -p 01-assembly 02-demultiplex 99-log runs tables
-# link base reference
-ln -s $REFERENCE_BASE bdr
-# link raw sequences data
-for i in `ls $FOLDER_INPUT*fastq.gz`;
-do name=`basename $i` ;
-ln -s $i raw/$name ;
-done
-# link barcode data
-for i in `ls $FOLDER_INPUT*dat`;
-do name=`basename $i` ;
-ln -s $i barcodes/$name ;
-done
-# run pipeline
-snakemake -s scripts/step1.sf -j $CORES --latency-wait 120
-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 $CORES --latency-wait 120
-
-## this work !
-
-mkdir -p 01-assembly 02-demultiplex/02-01-raw 02-demultiplex/02-02-filtered 02-demultiplex/02-03-cleaned 99-log 03-filtered
-
+## assemble & demultiplex
 cd 01-assembly
 snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
 cd ..
+## filter sequences
 cd 02-demultiplex
-snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
+snakemake -s Snakefile -j 8 --dry-run --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
+cd ..
+## concatenate samples into run
+for run in `ls 02-demultiplex/03-cleaned/`;
+do cat 02-demultiplex/03-cleaned/${run}/*.c.r.l.u.fasta > 03-filtered/01-runs/${run}_run.fasta ;
+done
+## taxonomic assignation & format
+cd 03-filtered
+snakemake -s Snakefile -j 8 --dry-run --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
+cd ..
 
 
 ## clean
 snakemake -s Snakefile --delete-all-output --dry-run
 snakemake -s Snakefile --delete-all-output
+