Nextflow Pipeline Runner
Run nf-core bioinformatics pipelines for RNA-seq, WGS, and ATAC-seq analysis
You have RNA-seq FASTQ files and know nf-core has a pipeline for it, but the parameter combinations are overwhelming, your config keeps failing on your cluster, and the documentation assumes you already know Nextflow. Your PI wants results, not pipeline debugging.
Who it's for: bioinformaticians running nf-core pipelines on institutional clusters, wet-lab researchers analyzing their own sequencing data, graduate students learning computational biology workflows, core facility staff processing samples for multiple PIs, clinical bioinformatics teams running validated analysis pipelines
Example
"Run nf-core/rnaseq on these 24 samples with our SLURM cluster" → Complete Nextflow config for your cluster, sample sheet from your file naming convention, pipeline launch command with optimized parameters, and results interpretation guide for differential expression outputs
CLAUDE.md Template
New here? 3-minute setup guide → | Already set up? Copy the template below.
npx ccplaybooks add nextflow-pipeline-runner# nf-core Pipeline Deployment
Run nf-core bioinformatics pipelines on local or public sequencing data.
**Target users:** Bench scientists and researchers without specialized bioinformatics training who need to run large-scale omics analyses—differential expression, variant calling, or chromatin accessibility analysis.
## Workflow Checklist
```
- [ ] Step 0: Acquire data (if from GEO/SRA)
- [ ] Step 1: Environment check (MUST pass)
- [ ] Step 2: Select pipeline (confirm with user)Get new playbooks like this one
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What This Does
This playbook helps bench scientists and researchers run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data without specialized bioinformatics training. It handles everything from acquiring public datasets from GEO/SRA, through environment setup, samplesheet creation, pipeline execution, and output verification -- giving you a structured, step-by-step workflow for differential expression, variant calling, or chromatin accessibility analysis.
Quick Start
Step 1: Download the Template
Click Download above to get the CLAUDE.md file.
Step 2: Set Up Your Project
Create a project folder and place the template inside:
my-bioinformatics-project/
CLAUDE.md
fastq/ # Your FASTQ files (or will be downloaded)
Step 3: Start Working
claude
Say: "I have RNA-seq FASTQ files in the fastq/ directory. Help me run the nf-core rnaseq pipeline with the GRCh38 genome."
Workflow Overview
The playbook follows a structured 7-step checklist:
- Acquire Data -- Download from GEO/SRA if using public datasets (skip for local files)
- Environment Check -- Verify Docker, Nextflow, and Java are properly installed
- Select Pipeline -- Choose rnaseq, sarek, or atacseq based on your data type
- Run Test Profile -- Validate your environment with a small test dataset
- Create Samplesheet -- Auto-generate or validate your sample metadata CSV
- Configure & Run -- Set genome, aligner, and resource limits, then execute
- Verify Outputs -- Check for successful completion and locate key result files
Supported Pipelines
| Data Type | Pipeline | Version | Goal |
|---|---|---|---|
| RNA-seq | rnaseq |
3.22.2 | Gene expression |
| WGS/WES | sarek |
3.7.1 | Variant calling |
| ATAC-seq | atacseq |
2.1.2 | Chromatin accessibility |
Tips
- Always run the test profile before processing real data to catch environment issues early
- Use
-resumeto continue from checkpoints if a run fails partway through - For HPC environments, swap
-profile dockerfor-profile singularity - Set resource limits (
--max_cpus,--max_memory,--max_time) to match your machine
Key Outputs
RNA-seq: Gene count matrices and TPM values in results/star_salmon/
WGS/WES (Sarek): VCF variant files in results/variant_calling/
ATAC-seq: Peak calls in results/macs2/narrowPeak/ and coverage tracks in results/bwa/mergedLibrary/bigwig/
All pipelines produce a MultiQC report at results/multiqc/multiqc_report.html.
Example Prompts
"I have RNA-seq FASTQ files in ./data/. Run the nf-core rnaseq pipeline with GRCh38."
"Download GSE110004 from GEO and run differential expression analysis."
"Check my environment and run the sarek test profile for variant calling."
"Create a samplesheet from FASTQ files in ./fastq/ for the atacseq pipeline."
"Resume my failed rnaseq pipeline run."