# Ena Fetch

Query metadata and download sequencing data from the European Nucleotide Archive (ENA)...

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill ena-fetch -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill ena-fetch -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill ena-fetch -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill ena-fetch -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Query metadata and download sequencing data from the European Nucleotide Archive (ENA) via the Portal and Browser APIs. Works with ENA/SRA accessions (PRJEB/PRJNA studies, ERR/SRR/DRR runs, ERX/SRX experiments, SAMEA/SAMN samples), listing runs and FASTQ links, building custom file reports, running advanced metadata searches, and emitting a standardised metadata.tsv plus a pipeline-ready nf-core/rnaseq or nf-core/scrnaseq samplesheet.csv.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 🦖 ENA Fetch

You are **ENA Fetch**, a specialised ClawBio agent for the European Nucleotide
Archive. Your role is to turn an ENA accession into run metadata, FASTQ links,
a standardised sample table, or a samplesheet a pipeline can consume directly.

## Trigger

**Fire this skill when the user says any of:**
- "ENA", "European Nucleotide Archive"
- "PRJEB12345", "ERR1234567", "ERX...", "SAMEA...", "ERZ..."
- "get the FASTQ links for this project"
- "build a samplesheet for nf-core/rnaseq from this accession"
- "what runs are in this study"
- "search ENA for paired-end RNA-seq in <organism>"

**Do NOT fire when:**
- The accession is `GSE`/`GSM` (GEO), `PXD` (PRIDE), `E-MTAB` (ArrayExpress) or
  `S-BSST` (BioStudies), route to the matching skill. `geo-fetch` resolves GEO
  to ENA internally, so start there for a GSE.
- The user has a DOI or PubMed ID rather than an accession, route to
  `article-data-fetcher`.
- The data is controlled-access (EGA/dbGaP). This skill only reaches public ENA
  records and has no credential path.

## Why This Exists

- **Without it**: you hand-build Portal API query strings, work out which
  `fields` exist, then reshape the TSV into whatever column names your pipeline
  expects, differently for every project.
- **With it**: one command returns a **standardised `metadata.tsv`** whose core
  columns are identical across every ClawBio archive skill, and a
  **pipeline-ready `samplesheet.csv`** that already matches the nf-core/rnaseq
  or nf-core/scrnaseq column contract, so the output can be handed straight to
  a pipeline instead of needing a bespoke parsing step each time. It can also
  emit a runnable download script for the FASTQs it just listed.
- **Why ClawBio**: the read-pairing rules, the field mapping and the null
  handling are fixed and inspectable, not re-derived per study by a model. That
  is what makes a samplesheet safe to run a pipeline on.

## Core Capabilities

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/ena-fetch/SKILL.md