Merge pull request #5 from JD2112/devel

Devel

Author: JD2112

.github/credit_breakdown.md

@@ -0,0 +1,18 @@
+## 🛠️ Contribution Breakdown
+
+### Conceptualization
+
+| Role               | Name & Link                                                                | Description                                                                                       |
+|--------------------|-----------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------|
+| **Conceptualization** | [Jyotirmoy Das](https://github.com/JD2112)                                  | Lead design and conceptual framework of the **TwistMethNext** pipeline. Developed the overall approach and strategy for DNA methylation data analysis. |
+| **Development**      | [Jyotirmoy Das](https://github.com/JD2112)                                  | Developed core functionality of the pipeline, integrated tools like **Bismark** and **methylKit** for downstream analysis. |
+|       | External Contributors                                                       | Contributions to specific modules, bug fixes, and documentation updates are highly appreciated.     |
+| **Implementation**   | [Jyotirmoy Das](https://github.com/JD2112)                                  | Implemented the pipeline in **Nextflow**, ensured scalability, flexibility, and compatibility with NGS workflows. Integrated **FastQC**, **Trim Galore**, and other quality control tools. |
+|    | Collaborators                                                              | Assisted in optimizing the pipeline's performance for large-scale datasets and adapting it to different computational environments. |
+| **Testing & Validation** | [Jyotirmoy Das](https://github.com/JD2112)                                  | Validated the pipeline’s correctness, tested with synthetic datasets, and ensured robust error handling. Conducted performance testing. |
+|  | External Users                                                            | Early adopters and collaborators who contributed feedback, bug reports, and insights for improving the robustness and accuracy. |
+| **Documentation**    | [Jyotirmoy Das](https://github.com/JD2112)                                  | Authored documentation, including the user manual and installation guide. Ensured clarity and ease of use. |
+|    | Contributors                                                               | External contributions to documentation for clarifications, additional use cases, and examples.     |
+
+
+---

.github/workflows/build-docs.yml

@@ -38,6 +38,9 @@ jobs:
           git config --global user.name "${{ github.actor }}"
           git config --global user.email "${{ github.actor }}@users.noreply.github.com"
 
+      - name: Inject current year into mkdocs.yml
+        run: python update_year.py
+        
       - name: Cache mkdocs builds
         uses: actions/cache@v3
         with:

.gitignore

@@ -3,12 +3,13 @@ work/
 .DS_Store
 .nextflow/
 pipeline_info/
-docs/
 *.sif
 Results/
 # workflows/
 data/*.gtf
 data/*.gz
 *.dot
 protocols/
-nf-results/
+nf-results/
+files-dump/
+instructions.md

conf/base.config

@@ -39,9 +39,9 @@ timeline {
   }
 
 manifest {
-    name            = 'TwistNext'
+    name            = 'TwistMethNext'
     author          = 'Jyotirmoy Das'
-    homePage        = 'https://github.com/JD2112/TwistNext'
+    homePage        = 'https://github.com/JD2112/TwistMethNext'
     description     = 'Twist NGS DNA Methylation Data Analysis'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'

docs/README.md

@@ -1,26 +1,54 @@
 # Credits
 
-### Credits
+## 👤 Authors and Maintainers
 
-* Main Author:
-  * Jyotirmoy Das ([@JD2112](https://github.com/JD2112))
-* Maintainers:
-* Contributions:
+| Role         | Name & Link                                                                 | Description                                                                                      |
+|--------------|------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------|
+| **Main Author** | [Jyotirmoy Das](https://github.com/JD2112)                                  | Lead designer, developer, and overall coordinator for the **TwistMethNext** pipeline.           |
+| **Maintainer**  | [Jyotirmoy Das](https://github.com/JD2112)                                  | Actively maintaining the pipeline, fixing bugs, and implementing new features.                  |
+| **Contributors**| [All Contributors](https://github.com/JD2112/TwistMethNext/pulls)           | Thanks to everyone who helped in development, testing, and enhancement. Contributions welcome!  |
 
-### Citation
+---
 
-Das, J. (2024). TwistNext (v1.0.0). Zenodo.[ https://doi.org/10.5281/zenodo.14204261](https://doi.org/10.5281/zenodo.14204261)
+## 📄 Citation
 
-### HELP/FAQ/Troubleshooting
+If you use **TwistMethNext** in your work, please cite:
 
-Please check the [manual](usage/) for details.
+> Das, J. (2024). *TwistMethNext (v1.0.0)*. Zenodo. [https://doi.org/10.5281/zenodo.14204261](https://doi.org/10.5281/zenodo.14204261)
 
-Please create[ issues](https://github.com/JD2112/TwistNext/issues) on github.
+---
 
-### License(s)
+## ❓ Help, FAQ, Troubleshooting
 
-[GNU-3 public license](../LICENSE).
+- Refer to the [User Manual](index.md) for detailed usage instructions and guidance.
+- For bug reports, questions, or feature requests, please open an [issue on GitHub](https://github.com/JD2112/TwistMethNext/issues).
 
-### Acknowledgement
+---
 
-[**Core Facility, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden**](https://liu.se/en/organisation/liu/medfak/coref) and [**Clinical Genomics Linköping, Science for Life Laboratory, Sweden**](https://www.scilifelab.se/units/clinical-genomics-linkoping/).
+## 📜 License
+
+This project is licensed under the terms of the **GNU General Public License v3.0**.  
+
+---
+
+## 🙏 Acknowledgements
+
+### Research Institutions
+
+- **Core Facility, Faculty of Medicine and Health Sciences, Linköping University**  
+  [Linköping University Core Facility](https://liu.se/en/organisation/liu/medfak/coref)
+
+- **Clinical Genomics Linköping, Science for Life Laboratory, Sweden**  
+  [Clinical Genomics Linköping](https://www.scilifelab.se/units/clinical-genomics-linkoping/)
+
+- **National Academic Infrastructure for Supercomputing in Sweden (NAISS)**
+  > The computations/data storage were enabled by resources provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS), partially funded by the Swedish Research Council through grant agreement no. 2022-06725.
+
+These institutions provided invaluable resources and support for the development and testing of the TwistMethNext pipeline.
+
+### Additional Thanks
+
+- **Open Source Community**: Special thanks to the developers and contributors of [Nextflow](https://www.nextflow.io/), [Bismark](https://www.bioinformatics.babraham.ac.uk/projects/bismark/), [methylKit](https://github.com/observer101/methylKit), [EdgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html) and other bioinformatics tools integrated into this pipeline.
+- **Users and Testers**: A heartfelt thank you to all the early adopters, testers, and collaborators who helped refine and improve the tool through their feedback and bug reports.
+
+---