fix(readme): minor documentation changes

CITATION.cff

@@ -8,7 +8,7 @@ authors:
     given-names: 'Shabarinath'
     orcid: 'https://orcid.org/0000-0002-6713-1705'
 title: 'ExfilMS'
-version: 1.2.4
+version: 1.2.5
 abstract: 'ExfilMS is a cross-platform, command line interface (CLI) tool to extract mass spectrometry (MS) data from mzML formatted files, with filtering capabilities.'
 keywords:
   - 'mass spectrometry'

README.md

@@ -1,10 +1,10 @@
 ![ExfilMS](./img/logo.png)\
-[![NPM version][npm-image]][npm-url]
-[![license][license-image]][license-url]
-[![CI status][ci-image]][ci-url]
-[![test coverage][codecov-image]][codecov-url]
-[![semantic release][semantic-image]][semantic-url]
-[![npm download][download-image]][download-url]
+[![NPM][npm-image]][npm-url]
+[![License][license-image]][license-url]
+[![CI/CD][cicd-image]][cicd-url]
+[![CodeCov][codecov-image]][codecov-url]
+[![Semantic-Release][semantic-image]][semantic-url]
+[![Downloads][downloads-image]][downloads-url]
 [![DOI-Zenodo][doi-zenodo-image]][doi-zenodo-url]
 
 ## Introduction
@@ -120,11 +120,11 @@ $ docker build -t exfilms .
 ### CLI
 
 ```md
-# Using command line arguments
+# Using command line flags
 
 $ exfilms -i "/path/to/input/directory/containing/mzML/data/files/" ...
 
-# Interactive
+# Running interactive mode
 
 $ exfilms -x
 ```
@@ -134,11 +134,11 @@ $ exfilms -x
 ### Docker
 
 ```md
-# Using command line arguments
+# Using command line flags
 
 $ docker run --rm -it -v "/path/to/input/directory/":/inputDirectory -v "/path/to/output/directory/":/outputDirectory -v "/path/to/log/directory/":/logDirectory exfilms -i /inputDirectory -o /outputDirectory -l /logDirectory ....
 
-# Interactive
+# Running interactive mode
 
 $ docker run --rm -it -v "/path/to/input/directory/":/inputDirectory -v "/path/to/output/directory/":/outputDirectory -v "/path/to/log/directory/":/logDirectory exfilms -x
 ```
@@ -168,47 +168,47 @@ For more guidance on how to use ExfilMS, please refer to our available guides be
 
 > [!WARNING]
 >
-> 1. Unable to extract MS data from Bruker EVOQ instruments and SCIEX wiff2 scan files (unsupported format by ProteoWizard).
+> 1. Unable to extract MS data from Bruker EVOQ instruments and SCIEX wiff2 scan files (Unsupported file formats by ProteoWizard).
 >
 > 2. Unable to parse mzML data with a file size > 2GB.
 >
 > 3. Large MS data may cause Node environment to terminate abruptly due to memory limit exhaustion.
 >
-> 4. Slow output write speed due to build architecture difference (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker.
+> 4. May have slow output write speed due to build architecture difference (i.e, Intel vs AMD vs ARM) when running ExfilMS with Docker.
 >
-> 5. Unable to perform chromatography filtering as of now.
+> 5. Unable to perform chromatogram filtering as of now.
 
 <br>
 
 ## Citations
 
 If you use ExfilMS in your work, please cite it using the following:
 
-Nambiar, V., & Nambiar, S. (2024). ExfilMS (Version 1.2.4) [Computer software]. https://doi.org/10.5281/zenodo.10976761
+Nambiar, V., & Nambiar, S. (2024). ExfilMS (Version 1.2.5) [Computer software]. https://doi.org/10.5281/zenodo.10976761
 
 <br>
 
-<!-- ## API Documentation
-Please refer to our API documentation [here](https://vmalnathnambiar.github.io/exfilms/). -->
-
 ## License
 
 Please refer to our license information [here](./LICENSE).
 
+<!-- ## API Documentation
+Please refer to our API documentation [here](https://vmalnathnambiar.github.io/exfilms/). -->
+
 <!-- URLs used in the markdown document-->
 
 [npm-image]: https://img.shields.io/npm/v/exfilms.svg
 [npm-url]: https://www.npmjs.com/package/exfilms
 [license-image]: https://img.shields.io/badge/License-MIT-yellow.svg
 [license-url]: https://github.com/vmalnathnambiar/exfilms/blob/main/LICENSE
-[ci-image]: https://github.com/vmalnathnambiar/exfilms/actions/workflows/build-publish.yml/badge.svg
-[ci-url]: https://github.com/vmalnathnambiar/exfilms/actions/workflows/build-publish.yml
+[cicd-image]: https://github.com/vmalnathnambiar/exfilms/actions/workflows/build-publish.yml/badge.svg
+[cicd-url]: https://github.com/vmalnathnambiar/exfilms/actions/workflows/build-publish.yml
 [codecov-image]: https://codecov.io/gh/vmalnathnambiar/exfilms/graph/badge.svg?token=V8O80QXJ5S
 [codecov-url]: https://codecov.io/gh/vmalnathnambiar/exfilms
 [semantic-image]: https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release
 [semantic-url]: https://github.com/semantic-release/semantic-release
-[download-image]: https://img.shields.io/npm/dm/exfilms.svg
-[download-url]: https://www.npmjs.com/package/exfilms
+[downloads-image]: https://img.shields.io/npm/dm/exfilms.svg
+[downloads-url]: https://www.npmjs.com/package/exfilms
 [doi-zenodo-image]: https://zenodo.org/badge/DOI/10.5281/zenodo.10976761.svg
 [doi-zenodo-url]: https://doi.org/10.5281/zenodo.10976761
 [nodejs-url]: https://nodejs.org/en/download/

docs/how-to-exfilms-the-complete-guide.md

@@ -4,7 +4,7 @@
 
 1. [Introduction](#introduction)
 2. [Execution of ExfilMS and The Use of Flags](#execution-of-exfilms-and-the-use-of-flags)
-3. [Useful Commands](#useful-commands)
+3. [Useful Flags](#useful-flags)
    - [General](#general)
    - [Specifying Input Data](#specifying-input-data)
    - [Specifying Outputs](#specifying-outputs)
@@ -33,17 +33,17 @@ However, running this command on its own will result in an error, as seen below.
 
 ![launch-err](../img/launch/err-default.png)
 
-The `i`, `--inputDirectory` displayed in the error message is known as a command line argument (or "command" or "flag") that is required for the successful execution of ExfilMS. There are both required and non-required flags available for your use. The inclusion of these flags along with the `exfilms` command will configure and establish the behaviour of the tool for running its extraction (and filtering) process.
+The `i`, `--inputDirectory` displayed in the error message is known as a command line flag (or flag) that is required for the successful execution of ExfilMS. There are both required and non-required flags available for your use. The inclusion of these flags along with the `exfilms` command will configure and establish the behaviour of the tool for running its extraction (and filtering) process.
 
 <br>
 
-## Useful Commands
+## Useful Flags
 
 ### General
 
 `--help`
 
-Displays a list of available commands along with their descriptions. This is useful for understanding the purpose of each flag.
+Displays a list of available flags along with their descriptions. This is useful for understanding the purpose of each flag.
 
 ```md
 # Show help