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nextflow-development

Run nf-core bioinformatics pipelines on sequencing data with environment validation and output verification.

Updated Apr 8, 2026
Search Tags:#RNA-seq#ATAC-seq#nf-core#nextflow#bioinformatics pipelines#WGS WES#samplesheet generation
One-click install
npx skills add https://github.com/sun2443/designer-skills --skill nextflow-development-sun2443
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: nextflow-development
Source: https://github.com/sun2443/designer-skills/tree/main/bio-research/skills/nextflow-development
Command: npx skills add https://github.com/sun2443/designer-skills --skill nextflow-development-sun2443

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires yaml, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill removes the friction of running large nf-core bioinformatics workflows by guiding you from data acquisition through environment validation, pipeline selection, configuration, and output verification.

Core Features & Use Cases

  • Runs nf-core pipelines via Nextflow: Executes RNA-seq (rnaseq), WGS/WES (sarek), and ATAC-seq (atacseq) with version-pinned commands.
  • Handles both local files and public GEO/SRA datasets: Supports fetching GEO/SRA reads, generating samplesheets, and re-running with resume when needed.
  • Reduces setup failures with guardrails: Performs a pre-flight environment check (Docker/Nextflow/Java) and enforces a test profile run before full execution.
  • Produces user-ready outputs and verification steps: Points you to key result artifacts (e.g., MultiQC reports, gene counts/TPM tables, VCFs, peaks/BigWig).

Quick Start

Tell the AI to help you run the RNA-seq pipeline for your study by using your GEO accession to fetch data, generate the samplesheet, run the environment check, execute a test profile, then run nf-core/rnaseq with the correct genome and your confirmed settings.

Frequently Asked Questions about nextflow-development

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

FAQPage Schema
How do I run nf-core pipelines on GEO or SRA sequencing data?▼

You can run nf-core pipelines on GEO/SRA accessions by fetching the public reads, generating a compatible samplesheet, and executing a Nextflow run. The workflow validates the environment and constructs the deterministic command for end-to-end processing.

Can I use local FASTQ or BAM files to run an nf-core RNA-seq pipeline?▼

Yes, you can use local FASTQ or BAM files to run the nf-core RNA-seq pipeline. The skill validates local inputs, generates the required samplesheet, and executes the workflow while verifying outputs like MultiQC reports and gene count tables.

Do I need Docker and Java installed to run Nextflow bioinformatics pipelines?▼

Yes, Docker, Java, and Nextflow are required to run these bioinformatics pipelines. The skill performs a pre-flight environment check to ensure dependencies are installed before executing a mandatory passing test profile run.

How do I generate a samplesheet for WGS, WES, or ATAC-seq nf-core workflows?▼

Generating a samplesheet for WGS, WES, or ATAC-seq workflows involves validating input data and constructing a compatible file mapping. The skill creates and validates this samplesheet before executing pipeline-specific configurations for sarek or atacseq.

What is the best way to verify nf-core pipeline results like VCFs and peaks?▼

The best way to verify nf-core pipeline results like VCFs and peaks is to check for pipeline-specific result files and MultiQC reports. The skill executes output verification to confirm these artifacts are successfully generated after the run.

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