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fetchngs

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Fetch public FASTQ data with provenance

Education & Research#bioinformatics#metadata#nf-core#nextflow#sequencing#accession#fastq
Authordanilomonge
Version1.0.0
Installs0

System Documentation

What problem does it solve?

fetchngs removes the manual overhead of turning public sequencing accessions into downloadable metadata and raw FastQ files, while keeping runs reproducible and schema-validated.

Core Features & Use Cases

  • Accession-driven retrieval: Download data for SRA, ENA, DDBJ, GEO, and related public identifiers from a single input list.
  • Reproducible pipeline runs: Run pinned nf-core/fetchngs releases with Nextflow-aware version control and recorded provenance.
  • Downstream-ready outputs: Generate cleaned output directories, pipeline reports, and optional samplesheets for supported nf-core pipelines.
  • Use Case: A researcher has a list of accessions and wants one command to collect metadata, FastQ files, and run logs without guessing parameters.

Quick Start

Ask the fetchngs skill to process your accession list into an output directory using the desired profile, and specify a pipeline version only when you need a non-latest release.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: fetchngs
Download link: https://github.com/danilomonge/nf-claw/archive/main.zip#fetchngs

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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