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bamtofastq

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Run bam-to-fastq workflows with confidence

Software Engineering#workflow#provenance#bioinformatics#nf-core#nextflow#samplesheet#bamtofastq
Authordanilomonge
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This Skill removes the guesswork from running nf-core bamtofastq by turning a pinned bioinformatics workflow into a validated, reproducible, and agent-friendly execution plan.

Core Features & Use Cases

  • Fastq Conversion Workflow: Converts BAM or CRAM inputs into FASTQ outputs for downstream analysis.
  • Release-Aware Execution: Supports pinned pipeline releases, Nextflow version selection, and on-demand release documentation.
  • Production Guardrails: Enforces samplesheet structure, required parameters, allowed values, and provenance capture for safer runs.
  • Use Case: A researcher needs to convert many sequencing alignments into FASTQ files and rerun an older release with a specific Nextflow engine version for compatibility.

Quick Start

Ask the bamtofastq skill to run the pipeline for your samplesheet, output directory, and preferred environment profile.

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: bamtofastq
Download link: https://github.com/danilomonge/nf-claw/archive/main.zip#bamtofastq

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