diff --git a/CHANGELOG.md b/CHANGELOG.md index 653da944..8e1f2ac2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -44,7 +44,8 @@ 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 diff --git a/README.md b/README.md index 9419fa1a..9f59aec2 100644 --- a/README.md +++ b/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]