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nextflow-development

Run nf-core workflows on sequencing data to produce analysis-ready outputs and QC reports.

1|Updated Mar 30, 2026
Search Tags:#geo#nf-core#nextflow#sequencing#rnaseq#sra#samplesheet
One-click install
npx skills add https://github.com/ilove323/comlan-skills --skill nextflow-development-ilove323
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: nextflow-development
Source: https://github.com/ilove323/comlan-skills/tree/main/bio-research/skills/nextflow-development
Command: npx skills add https://github.com/ilove323/comlan-skills --skill nextflow-development-ilove323

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pyyaml, requests, awscli, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This skill helps laboratory researchers and analysts run nf-core Nextflow workflows without deep bioinformatics expertise by automating environment checks, data acquisition, samplesheet creation, genome reference management, test runs, and pipeline execution guidance.

Core Features & Use Cases

  • GEO/SRA acquisition: Inspect studies, select subsets, fetch FASTQ URLs and download via ENA with resumable transfers.
  • Environment validation: Pre-flight checks for Docker, Nextflow, Java, network and system resources with actionable fixes.
  • Samplesheet generation & inference: Auto-detect FASTQ/BAM/CRAM, pair reads, infer tumor/normal status, assign replicates, and validate samplesheets for rnaseq, sarek, and atacseq.
  • Genome management: Map organisms to iGenomes keys, check or download references, and emit Nextflow parameter suggestions.
  • Run orchestration: Provide test-profile commands, recommended Nextflow run templates, and troubleshooting guidance for rnaseq, sarek, and atacseq.
  • Use case: Reanalyze a published GEO dataset by fetching runs, generating a validated samplesheet, running the test profile, and launching an nf-core rnaseq or sarek execution.

Quick Start

Run nf-core rnaseq on the FASTQ files in ./fastq, generate a validated samplesheet, and save results to ./results using genome GRCh38.

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 sequencing data from GEO or SRA?▼

Run nf-core pipelines on GEO or SRA data by inspecting studies, selecting subsets, fetching FASTQ URLs, and downloading via ENA with resumable transfers before executing workflows like rnaseq or sarek.

How do I generate a validated samplesheet for nf-core rnaseq?▼

Generate a validated samplesheet for nf-core rnaseq by auto-detecting FASTQ or BAM files, pairing reads, inferring tumor or normal status, assigning replicates, and validating the structure for pipeline execution.

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

Running Nextflow workflows requires Docker, Nextflow, and Java, and this skill performs pre-flight environment checks for these dependencies while providing actionable fixes for resource constraints.

What is the best way to manage genome references for nf-core pipelines?▼

Manage genome references by mapping organisms to iGenomes keys, checking or downloading references automatically, and emitting Nextflow parameter suggestions to configure your pipeline run.

Can I process local CRAM files with nf-core sarek for variant calling?▼

You can process local CRAM files with nf-core sarek for variant calling, as the skill auto-detects FASTQ, BAM, and CRAM formats and constructs the appropriate Nextflow commands for execution.

Why does my nf-core test profile validation fail before pipeline execution?▼

Test profile validation may fail due to missing genome references, invalid samplesheet structure, or insufficient system resources, which the environment checks and samplesheet validation steps help identify and resolve.

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