docs: Add diagram and logo (#28)

* docs: Add workflow diagram * docs: Add logos
dalmolingroup · Nov 2, 2023 · 888556b · 888556b
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diff --git a/README.md b/README.md
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+[![nf-core CI](https://github.com/dalmolingroup/euryale/actions/workflows/ci.yml/badge.svg)](https://github.com/dalmolingroup/euryale/actions/workflows/ci.yml)
+[![docs](https://github.com/dalmolingroup/euryale/actions/workflows/docs.yml/badge.svg)](https://github.com/dalmolingroup/euryale/actions/workflows/docs.yml)
+
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-4bc7e2a.svg?labelColor=000000)](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 singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
+
+![EURYALE Logo](assets/euryale_logo.png)
+
 ## Introduction
 
 **dalmolingroup/euryale** is a pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on [MEDUSA](https://github.com/dalmolingroup/medusa).
@@ -6,6 +15,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## Pipeline summary
 
+<picture>
+
+  <source media="(prefers-color-scheme: dark)" srcset="./assets/euryale_workflow.drawio.png">
+  <img alt="EURYALE diagram" src="./assets/euryale_workflow.light.png">
+</picture>
+
 ### Pre-processing
 
 - Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
@@ -21,6 +36,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 ### Taxonomic classification
 
 - Sequence classification ([`Kaiju`](https://github.com/bioinformatics-centre/kaiju/))
+- (**WIP**) Sequence classification ([`Kraken2`](https://github.com/DerrickWood/kraken2))
 - Visualization ([`Krona`](https://github.com/marbl/Krona/wiki))
 
 ### Functional annotation

diff --git a/assets/euryale_logo.png b/assets/euryale_logo.png
diff --git a/assets/euryale_workflow.drawio.png b/assets/euryale_workflow.drawio.png
diff --git a/assets/euryale_workflow.light.png b/assets/euryale_workflow.light.png
diff --git a/docs/assets/euryale_logo.png b/docs/assets/euryale_logo.png
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+../../assets/euryale_logo.png
diff --git a/docs/assets/euryale_workflow.drawio.png b/docs/assets/euryale_workflow.drawio.png
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+../../assets/euryale_workflow.drawio.png
diff --git a/docs/assets/euryale_workflow.light.png b/docs/assets/euryale_workflow.light.png
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+../../assets/euryale_workflow.light.png
diff --git a/docs/images/mqc_fastqc_adapter.png → docs/assets/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png → docs/assets/mqc_fastqc_adapter.png
diff --git a/docs/images/mqc_fastqc_counts.png → docs/assets/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png → docs/assets/mqc_fastqc_counts.png
diff --git a/docs/images/mqc_fastqc_quality.png → docs/assets/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png → docs/assets/mqc_fastqc_quality.png