Update README.md

README.md

@@ -1,14 +1,13 @@
 # pyigmap
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11103554.svg)](https://doi.org/10.5281/zenodo.11103554)
-
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with podman](https://img.shields.io/badge/run%20with-podman-892CA0?labelColo=000000&logo=podman)](https://podman.io/)
 
 ## Introduction
 
-`pyIgMap` is a [Nextflow](https://github.com/nextflow-io/nextflow)-driven and Python-based workflow for extracting and summarizing antigen receptor gene rearrangements from sequencing data.
+`pyIgMap` is a [Nextflow](https://github.com/nextflow-io/nextflow)-driven and Python-based pipeline for extracting and summarizing antigen receptor gene rearrangements from sequencing data.
 
 > [!NOTE]
 > The pipeline is built upon open source components commonly used for AIRR-seq data processing. The output is provided in [AIRR format](https://docs.airr-community.org/en/stable/) enabling downstream analysis with AIRR-compliant software such as [Immcantation](https://immcantation.readthedocs.io/en/stable/index.html).
@@ -19,48 +18,48 @@
 
 ## Quick start
 
-1. Clone a repository:
+1. This pipeline requires [Docker](https://docs.docker.com/engine/install/) or [Podman](https://podman.io/), [Java 11 (or later, up to 21)](http://www.oracle.com/technetwork/java/javase/downloads/index.html), [Bash](https://www.gnu.org/software/bash/) and [Make](https://www.gnu.org/software/make/) tool.
 
-```bash
-git clone https://github.com/BostonGene/pyigmap.git
-cd pyigmap
-```
+> [!NOTE]
+> To install the [Make](https://www.gnu.org/software/make/) tool execute: ```sudo apt install make```
 
-2. This workflow requires [Docker](https://docs.docker.com/engine/install/) or [Podman](https://podman.io/), Bash 3.2 (or later) and [Java 11 (or later, up to 21)](http://www.oracle.com/technetwork/java/javase/downloads/index.html). You can install it manually or execute:
+2. Clone the repository and go inside:
 
 ```bash
-make install-docker # requirements: Ubuntu x64
-make install-podman # requirements: Ubuntu 20.10 and newer
-make install-java # requirements: Linux x64
+git clone https://github.com/BostonGene/pyigmap.git
+cd pyigmap
 ```
+
+> [!TIP]
+> If you have Ubuntu 20.10 (amd64) or higher, you can install requirements above using:  
+> ```make install-docker``` or ```make install-podman```  
+> ```make install-java```
 
-3. Run this command to install all dependencies:
+3. Install Nextflow, build V(D)J references and Docker container images with a single command:
 
 ```bash
-make # will use Docker as container engine
+make
 ```
+> [!TIP]
+> To use a [Podman](https://podman.io/) as a container engine, run: ```make ENGINE=podman```
 
-or
+4. Start running your own analysis!
 
 ```bash
-make ENGINE=podman # will use Podman as container engine
+./pyigmap -profile <docker/podman> \
+    --mode <amplicon/rnaseq> \
+    --fq1 "R1.fastq.gz" \
+    --fq2 "R2.fastq.gz" \
+    --outdir "./results"
 ```
 
-4. Start running your own analysis!
-
-```bash
-# for amplicon data
-./pyigmap --mode amplicon --fq1 /path/to/R1.fastq.gz --fq2 /path/to/R2.fastq.gz -profile docker
+## Pipeline summary
 
-# for RNASeq data
-./pyigmap --mode rnaseq --fq1 /path/to/R1.fastq.gz --fq2 /path/to/R2.fastq.gz -profile docker
+...
 
-# for public data by sample id
-./pyigmap --mode rnaseq --sample_id SRR3743469 --reads_to_process 200000 -profile docker
+## Pipeline parameters
 
-# for public data from ZENODO
-./pyigmap --mode rnaseq --zenodo --fq1 SRR3743469_R1.fastq.gz --fq2 SRR3743469_R2.fastq.gz --reads_to_process 200000 -profile docker
-```
+...
 
 ## Contributing