README touch ups

README.md

@@ -1,9 +1,9 @@
 ![Logo](https://cbg-ethz.github.io/V-pipe/img/logo.svg)
 
 [![bio.tools](https://img.shields.io/badge/bio-tools-blue.svg)](https://bio.tools/V-Pipe)
-[![Snakemake](https://img.shields.io/badge/snakemake-≥6.5.2-blue.svg)](https://snakemake.github.io/snakemake-workflow-catalog/?usage=cbg-ethz/V-pipe)
+[![Snakemake](https://img.shields.io/badge/snakemake-≥6.8.1-blue.svg)](https://snakemake.github.io/snakemake-workflow-catalog/?usage=cbg-ethz/V-pipe)
 [![Deploy Docker image](https://github.com/cbg-ethz/V-pipe/actions/workflows/deploy-docker.yaml/badge.svg)](https://github.com/cbg-ethz/V-pipe/pkgs/container/v-pipe)
-[![Tests](https://github.com/kpj/rwrap/actions/workflows/main.yml/badge.svg)](https://github.com/kpj/rwrap/actions/workflows/main.yml)
+[![Tests](https://github.com/cbg-ethz/V-pipe/actions/workflows/run_regression_tests.yaml/badge.svg)](https://github.com/cbg-ethz/V-pipe/actions/workflows/run_regression_tests.yaml)
 [![License: Apache-2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
 V-pipe is a workflow designed for the analysis of next generation sequencing (NGS) data from viral pathogens. It produces a number of results in a curated format (consensus sequences, SNV calls, local/global haplotypes).
@@ -12,12 +12,12 @@ V-pipe is written using the Snakemake workflow management system.
 
 ## Usage
 
-Different ways of initializing V-pipe are presented below.
+Different ways of initializing V-pipe are presented below. We strongly encourage you to deploy it [using the quick install script](#using-quick-install-script), as this our prefered method.
 
 V-pipe expects the input samples to be organized in a [two-level](config/#samples) directory hierarchy,
 and the sequencing reads must be provided in a sub-folder named `raw_data`. Further details can be found on the [website](https://cbg-ethz.github.io/V-pipe/usage/).
 
-We provide [virus-specific base configuration files](config/#virus_base_config) which contain handy defaults for, e.g., HIV and SARS-CoV-2. Set the virus in the general section of the configuration file:
+We provide [virus-specific base configuration files](config/#virus-base-config) which contain handy defaults for, e.g., HIV and SARS-CoV-2. Set the virus in the general section of the configuration file:
 ```yaml
 general:
   virus_base_config: hiv
@@ -101,6 +101,7 @@ snakemake --use-conda --jobs 4 --printshellcmds --dry-run
   VICUNA is a *de novo* assembly software designed for populations with high mutation rates. It is used to build an initial reference for mapping reads with ngshmmalign aligner when a `references/cohort_consensus.fasta` file is not provided. Further details can be found in the [wiki](https://github.com/cbg-ethz/V-pipe/wiki/getting-started#input-files) pages.
 
 ### Computational tools
+
 Other dependencies are managed by using isolated conda environments per rule, and below we list some of the computational tools integrated in V-pipe:
 
 - **[FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)**
@@ -111,10 +112,6 @@ Other dependencies are managed by using isolated conda environments per rule, an
 
   Trimming and clipping of reads is performed by PRINSEQ. It is currently the most versatile raw read processor with many customization options.
 
-- **[Vicuna](https://www.broadinstitute.org/viral-genomics/vicuna)**
-
-  Vicuna is a de novo assembler designed for generating rough reference contigs of viral NGS data. It can deal with the inherent heterogeneity such as high single-base heterogeneity and structural variants.
-
 - **[ngshmmalign](https://github.com/cbg-ethz/ngshmmalign)**
 
   We perform the alignment of the curated NGS data using our custom ngshmmalign that takes structural variants into account. It produces multiple consensus sequences that include either majority bases or ambiguous bases.