`ena_filereport`

Pack: ena · Endpoint: https://gateway.pipeworx.io/ena/mcp

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/ena_filereport for the schema, then POST the same URL with its arguments for the data.

List every sequencing data file behind an ENA accession, with direct FASTQ/BAM/CRAM download URLs, byte sizes and MD5 checksums. AUTHORITATIVE for “where do I actually download the reads for this study/run/sample” — give it a study accession (PRJEB37886, PRJNA…), run (ERR…, SRR…, DRR…), sample (SAMEA…, SAMN…) or experiment, and it returns one row per run with its files. The multi-file semicolon-separated upstream fields are split into arrays here, so a caller does not silently fetch only the first mate of a paired-end run.

Parameters

Name	Type	Required	Description
`accession`	string	yes	ENA/INSDC accession: study (PRJEB37886, PRJNA…), run (ERR…/SRR…/DRR…), sample (SAMEA…/SAMN…), experiment (ERX…/SRX…) or taxon id. Must match the pattern the chosen result type accepts.
`result`	string	no	Result type to report files for. Default read_run; also analysis, assembly, wgs_set.
`fields`	string	no	Comma-separated columns. Omit for a file-oriented default set (URLs, sizes, checksums).
`limit`	number	no	Maximum rows, 1-1000 (default 25).

Example call

Arguments

{
  "accession": "PRJEB37886",
  "limit": 3
}

curl

curl -X POST https://gateway.pipeworx.io/ena/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"ena_filereport","arguments":{"accession":"PRJEB37886","limit":3}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('ena_filereport', {
  "accession": "PRJEB37886",
  "limit": 3
});

More examples

{
  "accession": "PRJEB37886",
  "result": "read_run",
  "fields": "run_accession,fastq_ftp,fastq_bytes,submitted_format",
  "limit": 3
}

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "ena": {
      "url": "https://gateway.pipeworx.io/ena/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

ena_filereport