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nextflow-development

Automate nf-core pipeline execution for RNA-seq, WGS/WES, and ATAC-seq data.

1|Updated Mar 9, 2026
Search Tags:#workflow#bioinformatics#nf-core#nextflow#samplesheet#genome-suggestion
One-click install
npx skills add https://github.com/kiryteo/opencode-setup --skill nextflow-development-kiryteo
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: nextflow-development
Source: https://github.com/kiryteo/opencode-setup/tree/main/skills/nextflow-development
Command: npx skills add https://github.com/kiryteo/opencode-setup --skill nextflow-development-kiryteo

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires yaml, requests.

What problem does it solve?

Automates the setup and orchestration of nf-core pipelines (rnaseq, sarek, atacseq) for sequencing data, reducing manual configuration, errors, and repetitive tasks.

Core Features & Use Cases

  • Generate, validate, and manage nf-core samplesheets from sequencing data for both local FASTQs and public GEO/SRA datasets.
  • Suggest appropriate genomes and nf-core pipelines based on data type and metadata, and coordinate lightweight data acquisition workflows.
  • Integrate with environment checks and downstream run preparation to streamline end-to-end analyses.

Quick Start

Generate a samplesheet from your sequencing data and prepare a Nextflow nf-core run.

Frequently Asked Questions about nextflow-development

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
Can I use this skill to suggest the right reference genome for my sequencing data?▼

Yes, the skill suggests appropriate reference genomes based on your data type and metadata. It integrates genome suggestion workflows to ensure the correct genomic reference is selected before running nf-core pipelines.

How do I generate an nf-core samplesheet from local FASTQ files?▼

To generate an nf-core samplesheet from local FASTQ files, the skill automates samplesheet creation and validation by parsing your sequencing data. It prepares the necessary input configuration for Nextflow pipeline execution.

Can I use GEO or SRA accessions to automatically fetch data for nf-core pipelines?▼

Yes, you can use GEO or SRA accessions to fetch data for nf-core pipelines. The skill integrates lightweight data acquisition workflows to pull public sequencing datasets and automatically format them into validated samplesheets.

Which nf-core pipelines are supported for RNA-seq, WGS, and ATAC-seq analysis?▼

The supported nf-core pipelines include rnaseq, sarek, and atacseq. The skill suggests appropriate pipelines and genomes based on your sequencing data type and metadata to coordinate end-to-end analysis.

Do I need to manually configure Nextflow parameters to run nf-core pipelines?▼

No, you do not need to manually configure Nextflow parameters. The skill automates environment checks, run preparation, and pipeline orchestration to reduce manual setup and repetitive configuration tasks.

Can this skill suggest the right reference genome for my sequencing data?▼

Yes, the skill suggests appropriate reference genomes based on your data type and metadata. It integrates genome suggestion workflows to ensure the correct genomic reference is selected before running nf-core pipelines.

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