Update docs

Author: mrueda

.github/workflows/docker-build-multi-arch.yml

@@ -31,7 +31,7 @@ jobs:
         uses: docker/build-push-action@v4
         with:
           context: .
-          file: ./Dockerfile
+          file: ./docker/Dockerfile
           push: true
           tags: |
             manuelrueda/pheno-ranker:${{ steps.get_version.outputs.VERSION }}

.github/workflows/docker-build.yml

@@ -30,7 +30,7 @@ jobs:
 
       - name: Build Docker image
         run: |
-          docker build -t manuelrueda/pheno-ranker:${{ steps.get_version.outputs.VERSION }} .
+          docker build -f docker/Dockerfile -t manuelrueda/pheno-ranker:${{ steps.get_version.outputs.VERSION }} .
           docker tag manuelrueda/pheno-ranker:${{ steps.get_version.outputs.VERSION }} manuelrueda/pheno-ranker:latest
 
       - name: Login to Docker Hub

.github/workflows/test-docker-build-multi-arch.yml

@@ -31,7 +31,7 @@ jobs:
         uses: docker/build-push-action@v4
         with:
           context: .
-          file: ./Dockerfile
+          file: ./docker/Dockerfile
           push: true
           tags: |
             manuelrueda/pheno-ranker-test:${{ steps.get_version.outputs.VERSION }}

README.md

@@ -0,0 +1,165 @@
+<p align="center">
+  <a href="https://github.com/cnag-biomedical-informatics/pheno-ranker"><img src="https://raw.githubusercontent.com/cnag-biomedical-informatics/pheno-ranker/main/docs/img/PR-logo.png" width="400" alt="Pheno-Ranker"></a>
+</p>
+<p align="center">
+    <em>Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond</em>
+</p>
+
+[![Build and Test](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/build-and-test.yml)
+[![Coverage Status](https://coveralls.io/repos/github/CNAG-Biomedical-Informatics/pheno-ranker/badge.svg?branch=main)](https://coveralls.io/github/CNAG-Biomedical-Informatics/pheno-ranker?branch=main)
+[![CPAN Publish](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/cpan-publish.yml/badge.svg)](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/cpan-publish.yml)
+[![Kwalitee Score](https://cpants.cpanauthors.org/dist/Pheno-Ranker.svg)](https://cpants.cpanauthors.org/dist/Pheno-Ranker)
+![version](https://img.shields.io/badge/version-{{VERSION}}-28a745)
+[![Docker Build](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/docker-build-multi-arch.yml/badge.svg)](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/docker-build-multi-arch.yml)
+[![Docker Pulls](https://badgen.net/docker/pulls/manuelrueda/pheno-ranker?icon=docker&label=pulls)](https://hub.docker.com/r/manuelrueda/pheno-ranker/)
+[![Docker Image Size](https://badgen.net/docker/size/manuelrueda/pheno-ranker?icon=docker&label=image%20size)](https://hub.docker.com/r/manuelrueda/pheno-ranker/)
+[![Documentation Status](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/documentation.yml/badge.svg)](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/documentation.yml)
+[![License](https://img.shields.io/badge/License-Artistic%202.0-0298c3.svg)](https://opensource.org/licenses/Artistic-2.0)
+[![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1n3Etu4fnwuDWNveSMb1SzuN50O2a05Rg)
+
+---
+
+**📘 Documentation:** <a href="https://cnag-biomedical-informatics.github.io/pheno-ranker" target="_blank">https://cnag-biomedical-informatics.github.io/pheno-ranker</a>
+
+**📖 Usage:** <a href="https://cnag-biomedical-informatics.github.io/pheno-ranker/usage/" target="_blank">https://cnag-biomedical-informatics.github.io/pheno-ranker/usage/</a>
+
+**📓 Google Colab tutorial:** <a href="https://colab.research.google.com/drive/1n3Etu4fnwuDWNveSMb1SzuN50O2a05Rg" target="_blank">https://colab.research.google.com/drive/1n3Etu4fnwuDWNveSMb1SzuN50O2a05Rg</a>
+
+**📦 CPAN Distribution:** <a href="https://metacpan.org/pod/Pheno::Ranker" target="_blank">https://metacpan.org/pod/Pheno::Ranker</a>
+
+**🐳 Docker Hub Image:** <a href="https://hub.docker.com/r/manuelrueda/pheno-ranker/tags" target="_blank">https://hub.docker.com/r/manuelrueda/pheno-ranker/tags</a>
+
+**🌐 Web App UI:** <a href="https://pheno-ranker.cnag.eu" target="_blank">https://pheno-ranker.cnag.eu</a>
+
+---
+
+# Pheno-Ranker
+
+`Pheno-Ranker` is a lightweight toolkit for semantic similarity analysis of phenotypic, clinical, and other categorical data serialized as `JSON`, `YAML`, or preprocessed `CSV`.
+
+It supports GA4GH-oriented formats such as Beacon Friendly Format (`BFF`) and Phenotype Exchange Format (`PXF`), but it can also rank and compare generic JSON records beyond the biomedical domain.
+
+## What It Does
+
+`Pheno-Ranker` turns hierarchical records into comparable binary vectors and computes pairwise similarity or distance metrics.
+
+Main workflows:
+
+- **Cohort mode**: compare every individual or record against every other record in one or more cohorts.
+- **Patient mode**: rank records in a reference cohort against a target patient or object.
+- **Generic JSON mode**: compare arbitrary categorical JSON data using a configuration file.
+- **Precomputed mode**: reuse exported reference-cohort vectors for faster repeated patient matching.
+
+## Quick Start
+
+Basic cohort comparison:
+
+```bash
+pheno-ranker -r individuals.json
+```
+
+Patient matching:
+
+```bash
+pheno-ranker -r individuals.json -t patient.json --max-out 10
+```
+
+Generic JSON with a custom configuration:
+
+```bash
+pheno-ranker -r movies.json --config movies_config.yaml --include-terms genre year
+```
+
+Sparse Matrix Market output for large cohorts:
+
+```bash
+pheno-ranker -r individuals.json --matrix-format mtx -o matrix.mtx
+```
+
+Cytoscape-compatible graph export with edge filtering:
+
+```bash
+pheno-ranker -r individuals.json --cytoscape-json graph.json --graph-max-weight 10
+```
+
+## Selected Features
+
+- Native support for `BFF` and `PXF` JSON/YAML inputs.
+- Generic JSON support through YAML/JSON configuration files.
+- Cohort and patient-ranking modes.
+- Hamming distance and Jaccard similarity.
+- Optional weighted comparisons.
+- Export of intermediate hashes and coverage statistics.
+- Sparse Matrix Market (`mtx`) output for large matrix workflows.
+- Direct Cytoscape-compatible graph export with edge thresholds.
+- QR-code utilities for compact encoded vector exchange.
+- Companion utilities for CSV import and BFF/PXF simulation.
+
+## Output Formats
+
+Common outputs include:
+
+- `matrix.txt`: dense pairwise comparison matrix.
+- `matrix.mtx`: sparse Matrix Market output when `--matrix-format mtx` is used.
+- `rank.txt`: patient-mode ranking output.
+- `graph.json`: Cytoscape-compatible graph output.
+- `graph_stats.txt`: graph summary statistics.
+- `export.*.json`: intermediate files for inspection or precomputed workflows.
+
+## Installation
+
+For CPAN installation:
+
+```bash
+cpanm Pheno::Ranker
+pheno-ranker --help
+```
+
+For repository-based development:
+
+```bash
+git clone https://github.com/cnag-biomedical-informatics/pheno-ranker.git
+cd pheno-ranker
+cpanm --notest --installdeps .
+bin/pheno-ranker --help
+```
+
+Docker images are also available from Docker Hub:
+
+```bash
+docker pull manuelrueda/pheno-ranker:latest
+```
+
+Detailed installation instructions are available in the documentation:
+
+- <https://cnag-biomedical-informatics.github.io/pheno-ranker/download-and-installation/>
+- Non-containerized install: <https://github.com/CNAG-Biomedical-Informatics/pheno-ranker/blob/main/non-containerized/README.md>
+- Docker install: <https://github.com/CNAG-Biomedical-Informatics/pheno-ranker/blob/main/docker/README.md>
+
+## Documentation
+
+Long-form documentation, tutorials, and use cases live in the documentation site:
+
+- [Usage](https://cnag-biomedical-informatics.github.io/pheno-ranker/usage/)
+- [Cohort mode](https://cnag-biomedical-informatics.github.io/pheno-ranker/cohort/)
+- [Patient mode](https://cnag-biomedical-informatics.github.io/pheno-ranker/patient/)
+- [Generic JSON tutorial](https://cnag-biomedical-informatics.github.io/pheno-ranker/generic-json/)
+- [CSV import](https://cnag-biomedical-informatics.github.io/pheno-ranker/csv-import/)
+
+The built-in CLI help remains available:
+
+```bash
+pheno-ranker --help
+```
+
+`--man` is deprecated and now points to the online usage documentation.
+
+## Citation
+
+If you use `Pheno-Ranker` in published work, please cite:
+
+Leist, I.C. et al. (2024). *Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond*. BMC Bioinformatics. <https://doi.org/10.1186/s12859-024-05993-2>
+
+## Author
+
+Manuel Rueda, PhD. CNAG: <https://www.cnag.eu>