readme update

README.md

@@ -120,6 +120,8 @@ workdir
 Useful parameters for each program are stored into the file [config.yaml](config.yaml)
 Before to run the workflow, you have to set your parameters. Please edit [config.yaml](config.yaml).
 
+Here an example of a config.yaml file:
+
 ```diff
 container:
   /workdir/obitools.simg
@@ -143,8 +145,9 @@ assign_taxon:
   fasta : /workdir/reference_database/db_embl_std.fasta
 ```
 
+Table of parameters into config.yaml file:
 
-parameters |  description   | software |  rule             | default value     | excepted type
+parameters |  descriptions   | softwares |  rules             | default values    | excepted type
 ---------|------------------|-------|------------------|---------|----
 container | absolute path of singularity container file `obitools.simg` | [singularity](https://singularity.lbl.gov/) | every rules need this container to work | /workdir/obitools.simg  | absolute path of `simg` file
 fastqFolderPath   | absolute path of a folder which contains pairend-end raw reads `.fastq.gz` files and the sample description `.dat` files. | [illuminapairedend](https://pythonhosted.org/OBITools/scripts/illuminapairedend.html?highlight=illumina#module-illuminapairedend), [ngsfilter](https://pythonhosted.org/OBITools/scripts/ngsfilter.html)  | illuminapairedend, assign_sequences | /workdir/edna_miseq_rawdata/  | absolute path of a folder
@@ -162,15 +165,65 @@ fasta | absolute path to the fasta file of the reference database | [ecotag](htt
 ## 3.3 Run the workflow into a single command
 
 ```
-bash main.sh /path/to/fastq_dat_files /path/to/reference_database 16
+CORES=16
+bash main.sh $CORES
 ```
-order of arguments is important : 1) path to the folder which contains paired-end raw reads files and sample description file 2) path to the folder which contains reference database files 3) number of available cores (here for instance 16 cores)
 
-that's it ! The workflow is running and crunching your data. Look for the log folder output folder after the workflow is finished. See [Results](#5-results) section.
+with `CORES` the number of available cores to apply parallelization on the workflow.
+
+that's it ! The workflow is running and crunching your data. Look for the [99-log](99-log) folder output folder after the workflow is finished. See [Results](#4-results) section.
+
 
 ## 3.4 Run the workflow step by step
 
-run the workflow step by step : open the file [main.sh](main.sh) to see details
+Open the file [main.sh](main.sh) to see details:
+
+### 3.4.1 Merge paired-end sequences and demultiplexing
+
+```
+CORES=16
+cd 01-assembly
+snakemake -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
+cd ..
+```
+Check intermediate files into [01-assembly](01-assembly) folder.  
+Demultiplexed files will be generated into [02-demultiplex/01-raw](02-demultiplex/01-raw) folder.
+
+
+### 3.4.2 Filter sequences
+
+```
+CORES=16
+cd 02-demultiplex
+snakemake -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
+cd ..
+```
+
+Check intermediate files into [02-demultiplex](02-demultiplex) folder.  
+Check filtered sequences into [02-demultiplex/03-cleaned](02-demultiplex/03-cleaned) folder.
+
+
+### 3.4.3 Concatenate sample files into run files
+
+```
+for run in `ls 02-demultiplex/03-cleaned/`;
+do cat 02-demultiplex/03-cleaned/${run}/*.c.r.l.u.fasta > 03-filtered/01-runs/${run}_run.fasta ;
+done
+```
+
+Check concatened `{run}` files into [03-filtered/01-runs/](03-filtered/01-runs/) folder.
+
+### 3.4.4 Taxonomic assignation and format fasta files into tables
+
+```
+CORES=16 
+cd 03-filtered
+snakemake -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
+cd ..
+```
+Check intermediate files into [03-filtered](03-filtered) folder.  
+Final tables will be generated into [04-final_tables](04-final_tables) folder.
+
 
 
 # 4. Results

main.sh

@@ -13,21 +13,22 @@
 ## 
 ###############################################################################
 ## Usage:
-##    bash main.sh
+##    CORE=16
+##    bash main.sh $CORES
 ##
 ##
 ###############################################################################
-
+CORES=$1
 
 ###############################################################################
 ## assemble & demultiplex
 cd 01-assembly
-snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
+snakemake -s Snakefile -j $CORES --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 $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
 cd ..
 ###############################################################################
 ## concatenate samples into run
@@ -38,7 +39,7 @@ 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
-snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
+snakemake -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 120
 cd ..
 
 ###############################################################################