Merge pull request #268 from adamrtalbot/add_flow_diagram

Add Mermaid diagram

CHANGELOG.md

@@ -45,7 +45,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #264](https://github.com/nf-core/fetchngs/pull/264) - Remove synapse workflow from pipeline
 - [PR #265](https://github.com/nf-core/fetchngs/pull/265) - Use "+" syntax for profiles to accumulate profiles in nf-test
 - [PR #266](https://github.com/nf-core/fetchngs/pull/266) - Make .gitignore match template
-- [PR #273](https://github.com/nf-core/fetchngs/pull/273) - Update subworkflows
+- [PR #268](https://github.com/nf-core/fetchngs/pull/268) - Add mermaid diagram
+- [PR #273](https://github.com/nf-core/fetchngs/pull/273) - Update utility subworkflows
 
 ### Software dependencies
 

README.md

@@ -23,6 +23,35 @@
 
 **nf-core/fetchngs** is a bioinformatics pipeline to fetch metadata and raw FastQ files from both public and private databases. At present, the pipeline supports SRA / ENA / DDBJ / GEO / Synapse ids (see [usage docs](https://nf-co.re/fetchngs/usage#introduction)).
 
+```mermaid
+flowchart LR
+    IDS("Input
+    File") --> SRA & GEO & ENA & DDBJ
+    subgraph SG_DBIDS[Database IDs]
+      SRA("SRA")
+      GEO("GEO")
+      ENA("ENA")
+      DDBJ("DDBJ")
+    end
+    subgraph SG_METADATA[Download Metadata]
+      SRA & GEO & ENA & DDBJ --> META("Get
+      Metadata")
+      META --> LINKS("Get
+      Download
+      Links")
+    end
+    subgraph SG_FETCH_FASTQ[Download FastQ]
+      LINKS --> |--download_method 'ftp' | FTP("FTP")
+      LINKS --> |--download_method 'aspera' | ASPERA("Aspera")
+      LINKS --> |--download_method 'sratools' | SRATOOLS("sra-tools")
+    end
+    subgraph SG_FASTQ[Pipeline Outputs]
+      ASPERA & FTP & SRATOOLS --> FASTQ("FastQ")
+      FASTQ --> SAMPLESHEET("Samplesheet")
+    end
+    LINKS --> |--skip_fastq_download| SAMPLESHEET
+```
+
 ## Usage
 
 > [!NOTE]