update README for proper installation and usage

README.md

-# MetagenomicSnake
+# MetaSnk
 
 [![Snakemake](https://img.shields.io/badge/snakemake-≥5.4.4-brightgreen.svg)](https://snakemake.bitbucket.io)
 [![Build Status](https://travis-ci.org/snakemake-workflows/metagenomicsnake.svg?branch=master)](https://travis-ci.org/snakemake-workflows/metagenomicsnake)
 
 ## Description
 
-MetagenomicSnake is a Snakemake workflow for the analysis of metagenomic datasets from human microbiomes.
+MetaSnk is a modularized Snakemake workflow for the analysis of metagenomic datasets from human microbiomes.
+
+### Modules:
+ - [rawQC](README_rawQC.md)
+ - [preQC](README_preQC.md)
+ - taxProf
 
 ## Authors
 
@@ -17,8 +22,10 @@ MetagenomicSnake is a Snakemake workflow for the analysis of metagenomic dataset
 - Paired-end Illumina sequences
 
 ### Dependencies
-- Snakemake >= 5.4.4
+- Snakemake >= 5.5.0
 - Singularity >= 2.6
+- python >= 3.6.8
+- conda >= 4.6
 
 ## Usage
 
@@ -27,40 +34,61 @@ MetagenomicSnake is a Snakemake workflow for the analysis of metagenomic dataset
 #### Step 1: Install workflow
 
 If you simply want to use this workflow, download and extract the [latest release](https://github.com/snakemake-workflows/metagenomicsnake/releases).
+
+    git clone https://git.scicore.unibas.ch/TBRU/MetagenomicSnake.git path/to/MetaSnk
+    cd path/to/MetaSnk
+    echo -e "#MetaSnk directory\nmetasnk=$(pwd)\nexport metasnk">>$HOME/.bashrc
+    source $HOME/.bashrc
+
 If you intend to modify and further extend this workflow or want to work under version control, fork this repository as outlined in [Advanced](#advanced). The latter way is recommended.
 
 In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).
 
+#### Step 2: Create minimal environment
+
+Some rules will use this environment.
+
+    conda env create -f ./envs/MetaSnk.yaml
+
 #### Step 2: Configure workflow
 
 Configure the workflow according to your needs via editing the file `config.yaml`.
 
+##### Basic configuration
+- Make a copy of the config.yaml:
+```
+  cp ./config.yaml path/to/my_config.yaml
+```
+
 #### Step 3: Execute workflow
+Activate the environment via
+
+    conda activate MetaSnk
 
 Test your configuration by performing a dry-run via
 
-    snakemake --use-conda -n
+    snakemake --use-singularity -n
 
 Execute the workflow locally via
 
-    snakemake --use-conda --cores $N
+    snakemake --use-singularity --cores $N
 
-using `$N` cores or run it in a cluster environment via
+using `$N` cores or run it in a cluster environment controlled by SGE (Sun Grid Engine) via
 
-    snakemake --use-conda --cluster qsub --jobs 100
+    snakemake --use-singularity --cluster qsub --jobs 100
 
 or
 
-    snakemake --use-conda --drmaa --jobs 100
+    snakemake --use-singularity --drmaa --jobs 100
 
-If you not only want to fix the software stack but also the underlying OS, use
+or, in a cluster environment controlled by SLURM workload manager via
 
-    snakemake --use-conda --use-singularity
+    snakemake --profile ./profiles/slurm --use-singularity
 
 in combination with any of the modes above.
 See the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/executable.html) for further details.
 
-# Step 4: Investigate results
+#### Step 4: Investigate results
 
 After successful execution, you can create a self-contained interactive HTML report with all results via:
 
@@ -87,3 +115,5 @@ The following recipe provides established best practices for running and extendi
 ## Testing
 
 Tests cases are in the subfolder `.test`. They are automtically executed via continuous integration with Travis CI.
+
+snakemake --use-singularity -n -s Snakefile_test

README_preQC.md

+# MetaSnk: preQC
+
+## Description
+FastQC only performs a quality check but no QC processing is done. The **preQC**
+rule runs a multi-step pre-processing of the paired fastq files, it includes:
+
+- **trim_adapters**: adapter-trimming with "fastp". Fastp performs a quality check
+  and both paired fastq files are processed as follows\:
+
+    + remove adapters: here we provide the Nextera XT adapters,
+    + base correction in overlapped regions
+    + trimming of the last base in read 1
+    + discard reads shorter than a minimum length, after trimming
+    + a report with quality check, before and after processing
+- **filter_human**: removal of reads derived from human DNA with BBTools' [bbsplit]
+- **dedupe**: removal of duplicated reads with BBTools' [clumpify]
+- **trim_3end**: 3\'-end quality trimming with "fastp"
+- **concatenate_fastqs**: merges fastq files corresponding to the same sample into a single pair of fastq files
+- **summarize_preQC**: creates summarizing tables and plots
+
+[bbsplit]: http://seqanswers.com/forums/showthread.php?t=41288
+[clumpify]: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/clumpify-guide/
+
+<div style="text-align:center">
+  <img src="./images/preQC_dag.png"  width="350" height="500" />
+</div>
+
+## Usage
+
+### Case 1:
+From within the MetaSnk directory (i.e where it was installed, where the Snakefile is located):
+
+    snakemake --use-singularity --directory='path/to/workdir' -n preQC
+
+--directory : specifies the working directory and it is where snakemake will store its files for tracking the status of the workflow before/during/after execution.
+
+After preQC is completed we can generate a html report:
+
+    snakemake --directory='path/to/workdir' -n preQC_make_report
+
+The report will be created in the path specified for OUT_DIR in the configuration file.
+
+### Case2:
+Execute preQC from a working directory outside the MetaSnk directory:
+
+    snakemake --use-singularity -s path/to/MetaSnk/Snakefile -n preQC

README_rawQC.md

+# MetaSnk: rawQC
+
+## Description
+It runs FastQC on a random sample of R1 reads from the paired fastq-format files. MultiQC generates a single report per dataset.
+
+rawQC is an independent module, its output files are not required as inputs in other MetaSnk rules.
+
+<div style="text-align:center">
+  <img src="./images/rawQC_dag.png"  width="130" height="250" />
+</div>
+
+## Usage
+
+### Case 1:
+From within the MetaSnk directory (i.e where it was installed, where the Sbakefile is located):
+
+    snakemake --use-singularity --directory='path/to/workdir' -n rawQC
+
+--directory : specifies the working directory and it is where snakemake will store its files for tracking the status of the workflow before/during/after execution.
+
+After rawQC is completed we can generate a html report:
+
+    snakemake --directory='path/to/workdir' -n rawQC_make_report
+
+The report will be created in the path specified for OUT_DIR in the configuration file.
+
+### Case2:
+Execute rawQC from a working directory outside the MetaSnk directory:
+
+    snakemake --use-singularity -s path/to/MetaSnk/Snakefile -n rawQC