Merge pull request #29 from MPUSP/dev

docs: updating pipeline documentation and dag graph

Author: rabioinf

LICENSE

@@ -2,7 +2,7 @@
 
 MIT License
 
-Copyright (c) 2024, AUTHORS
+Copyright (c) 2025, Rina Ahmed-Begrich
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 

README.md

@@ -1,15 +1,16 @@
-# <a id="anchortitle" />Snakemake workflow: bacterial-rnaseq-preprocessing
+# <a id="anchortitle" />Snakemake workflow: bacterial-rnaseq-processing
 
+![Platform](https://img.shields.io/badge/platform-all-green)
 [![Snakemake](https://img.shields.io/badge/snakemake-≥8.0.0-brightgreen.svg)](https://snakemake.github.io)
-[![Tests](https://github.com/MPUSP/snakemake-bacterial-rnaseq-preprocessing/actions/workflows/main.yml/badge.svg)](https://github.com/MPUSP/snakemake-bacterial-rnaseq-preprocessing/actions/workflows/main.yml)
+[![Tests](https://github.com/MPUSP/snakemake-bacterial-rnaseq-processing/actions/workflows/main.yml/badge.svg)](https://github.com/MPUSP/snakemake-bacterial-rnaseq-processing/actions/workflows/main.yml)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![workflow catalog](https://img.shields.io/badge/Snakemake%20workflow%20catalog-darkgreen)](https://snakemake.github.io/snakemake-workflow-catalog)
 
 ------------------------------------------------------------------------
 
-A Snakemake workflow for the preprocessing of short read rnaseq data in bacteria.
+A Snakemake workflow for the processing of short read rnaseq data in bacteria.
 
--   [Bacterial RNAseq preprocessing](#anchortitle)
+-   [Bacterial RNAseq processing](#anchortitle)
     -   [Usage](#usage)
     -   [Workflow overview](#workflow-overview)
     -   [Installation](#installation)
@@ -22,13 +23,13 @@ A Snakemake workflow for the preprocessing of short read rnaseq data in bacteria
 
 ## Usage
 
-The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=MPUSP%2Fsnakemake-bacterial-rnaseq-preprocessing).
+The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=MPUSP%2Fsnakemake-bacterial-rnaseq-processing).
 
 If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) <repo>sitory and its DOI (see above).
 
 ## Workflow overview
 
-This workflow is a best-practice workflow for the preprocessing of short read sequencing data in bacteria. The workflow is built using [snakemake](https://snakemake.readthedocs.io/en/stable/) and consists of the following steps:
+This workflow is a best-practice workflow for the processing of short read sequencing data in bacteria. The workflow is built using [snakemake](https://snakemake.readthedocs.io/en/stable/) and consists of the following steps:
 
 1. Obtain genome database in `fasta` and `gff` format (`python`, [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/))
    1. Using automatic download from NCBI with a `RefSeq` ID
@@ -39,8 +40,9 @@ This workflow is a best-practice workflow for the preprocessing of short read se
 5. Map reads to the reference genome ([STAR aligner](https://github.com/alexdobin/STAR))
 6. Sort and index aligned rnaseq data ([Samtools](http://www.htslib.org/))
 7. Deduplicate reads by unique molecular identifier (UMI, [UMI-tools](https://umi-tools.readthedocs.io/en/latest/))
-8. Quantify biotype features ([featureCounts](https://subread.sourceforge.net/featureCounts.html))
-9. Generate summary report for all processing steps ([MultiQC](https://seqera.io/multiqc/))
+8. Generate cpm normalized coverage files ([deepTools](https://deeptools.readthedocs.io/en/latest/))
+9. Quantify biotype features ([featureCounts](https://subread.sourceforge.net/featureCounts.html))
+10. Generate summary report for all processing steps ([MultiQC](https://seqera.io/multiqc/))
 
 ---
 
@@ -52,8 +54,8 @@ This workflow is a best-practice workflow for the preprocessing of short read se
 **Step 1: Clone this repository**
 
 ``` bash
-git clone https://github.com/MPUSP/snakemake-bacterial-rnaseq-preprocessing.git
-cd snakemake-bacterial-rnaseq-preprocessing
+git clone https://github.com/MPUSP/snakemake-bacterial-rnaseq-processing.git
+cd snakemake-bacterial-rnaseq-processing
 ```
 
 **Step 2: Install dependencies**
@@ -62,12 +64,12 @@ It is recommended to install snakemake and run the workflow with `conda` or `mam
 
 **Step 3: Create snakemake environment**
 
-This step creates a new conda environment called `snakemake-bacterial-rnaseq-preprocessing`.
+This step creates a new conda environment called `snakemake-bacterial-rnaseq-processing`.
 
 ``` bash
 # create new environment with dependencies & activate it
-mamba create -c conda-forge -c bioconda -n snakemake-bacterial-rnaseq-preprocessing snakemake pandas python=3.12
-conda activate snakemake-bacterial-rnaseq-preprocessing
+mamba create -c conda-forge -c bioconda -n snakemake-bacterial-rnaseq-processing snakemake pandas python=3.12
+conda activate snakemake-bacterial-rnaseq-processing
 ```
 
 **Note:**
@@ -80,7 +82,7 @@ This step creates all conda environments specified in the snakemake rules. This
 
 ``` bash
 # activate new environment
-conda activate snakemake-bacterial-rnaseq-preprocessing
+conda activate snakemake-bacterial-rnaseq-processing
 snakemake -c 1 --sdm conda --conda-create-envs-only --conda-cleanup-pkgs cache
 ```
 
@@ -117,7 +119,7 @@ Currently, we support example configurations for three different sequencing prot
 To run the workflow from command line, change the working directory.
 
 ``` bash
-cd snakemake-bacterial-rnaseq-preprocessing
+cd snakemake-bacterial-rnaseq-processing
 ```
 
 To run the complete workflow with test files using **`conda`**, execute the following command. The definition of the number of compute cores is mandatory.