diff --git a/README.md b/README.md
index e205948..d2e1e22 100644
--- a/README.md
+++ b/README.md
@@ -8,24 +8,35 @@
-**ZARP** ([Zavolan-Lab][zavolan-lab] Automated RNA-Seq Pipeline) is a generic RNA-Seq analysis workflow that allows
-users to process and analyze Illumina short-read sequencing libraries with minimum effort. The workflow relies on
-publicly available bioinformatics tools and currently handles single or paired-end stranded bulk RNA-seq data.
-The workflow is developed in [Snakemake][snakemake], a widely used workflow management system in the bioinformatics
-community.
-
-According to the current ZARP implementation, reads are analyzed (pre-processed, aligned, quantified) with state-of-the-art
-tools to give meaningful initial insights into the quality and composition of an RNA-Seq library, reducing hands-on time for bioinformaticians and giving experimentalists the possibility to rapidly assess their data. Additional reports summarise the results of the individual steps and provide useful visualisations.
+**ZARP** ([Zavolab][zavolan-lab] Automated RNA-seq Pipeline) is a generic
+RNA-Seq analysis workflow that allows users to process and analyze Illumina
+short-read sequencing libraries with minimum effort. Better yet: With our
+companion [**ZARP-cli**](https://github.com/zavolanlab/zarp-cli) command line
+interface, you can start ZARP runs with the simplest and most intuitive
+commands.
+
+_RNA-seq analysis doesn't get simpler than that!_
+
+ZARP relies on publicly available bioinformatics tools and currently handles
+single or paired-end stranded bulk RNA-seq data. The workflow is developed in
+[Snakemake][snakemake], a widely used workflow management system in the
+bioinformatics community.
+
+ZARP will pre-process, align and quantify your single- or paired-end stranded
+bulk RNA-seq sequencing libraries with publicly available state-of-the-art
+bioinformatics tools. ZARP's browser-based rich reports and visualitations will
+give you meaningful initial insights in the quality and composition of your
+sequencing experiments - fast and simple. Whether you are an experimentalist
+struggling with large scale data analysis or an experienced bioinformatician,
+when there's RNA-seq data to analyze, just _zarp 'em_!
-
> **Note:** For a more detailed description of each step, please refer to the [workflow
> documentation][pipeline-documentation].
-
# Requirements
The workflow has been tested on:
@@ -39,6 +50,12 @@ The workflow has been tested on:
# Installation
+> **IMPORTANT: Rather than installing the ZARP workflow as described in this section, we
+> recommend installing [ZARP-cli](https://github.com/zavolanlab/zarp-cli) for most use
+> cases!** If you follow its [installation
+> instructions](https://zavolanlab.github.io/zarp-cli/guides/installation/), you can
+> skip the instructions below.
+
## 1. Clone the repository
Go to the desired directory/folder on your file system, then clone/get the
@@ -105,17 +122,6 @@ to include Singularity in the Conda environment:
mamba env update -f install/environment.root.yml
```
-### Command-line interface dependencies
-> A command-line interface, [ZARP-cli](https://github.com/zavolanlab/zarp-cli) is now availble and all you have to do to make use of it is update your environment:
-
-```bash
-mamba env update -f install/environment.cli.yml
-```
-
-More info at: [NEW: Running ZARP gets even easier!](#new-running-zarp-gets-even-easier)
-
-
-
## 4. Activate environment
Activate the Conda environment with:
@@ -177,22 +183,18 @@ bash tests/test_integration_workflow_with_conda/test.slurm.sh
# Running the workflow on your own samples
-## NEW: Running ZARP gets even easier!
-> You can now run your ZARP workflow using its' new command-line interface, [ZARP-cli](https://github.com/zavolanlab/zarp-cli). To enable ZARP-cli, simply install the additional dependencies by executing the following command _in your active Conda environment_:
+## Running ZARP with ZARP-cli (recommended)
-```bash
-mamba env update -f install/environment.cli.yml
-```
-Run:
-```
-zarp --help
-```
-to see the useful options available, or take a look at [ZARP-cli documentation](https://github.com/zavolanlab/zarp-cli)
+Head over to the [ZARP-cli](https://zavolanlab.github.io/zarp-cli/) to learn how to
+start ZARP runs with very simple commands, like:
+```sh
+zarp SRR23590181
+```
## Running ZARP without ZARP-cli
-1. Assuming that your current directory is the repository's root directory,
+1. Assuming that your current directory is the workflow repository's root directory,
create a directory for your workflow run and move into it with:
```bash
diff --git a/install/environment.cli.yml b/install/environment.cli.yml
deleted file mode 100644
index 65ff942..0000000
--- a/install/environment.cli.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-name: zarp
-channels:
- - conda-forge
- - bioconda
-dependencies:
- - zarp>=0.1