| id | nfcore_skills_index |
| name | nf-core Pipelines Skills Index |
| description | Skills for using nf-core community pipelines to process omics data,
from installation and configuration to running specific analysis pipelines.
|
nf-core Pipelines Skills
nf-core is a community-driven collection of 143+ curated
Nextflow pipelines for bioinformatics. All pipelines are open-source (MIT),
rigorously tested, and run portably on laptops, HPCs, and cloud platforms with
automated dependency management via Docker, Singularity, or Conda.
Available Skills
Getting Started & Usage
Installation, configuration, and common usage patterns for running any
nf-core pipeline on local machines, HPC clusters, or cloud environments.
Skill file: nfcore_usage.md
When to use:
- First time setting up Nextflow and nf-core
- Configuring pipelines for your HPC cluster or cloud environment
- Understanding resource management, resume, and offline execution
- Looking up nf-core CLI tool commands
Single-Cell & Bulk RNA-seq Pipelines
Pipelines for processing single-cell RNA-seq (10x, Drop-seq, Smart-seq)
and bulk RNA-seq data from raw FASTQs to count matrices.
Skill file: nfcore_transcriptomics.md
When to use:
- Processing 10x Chromium, Drop-seq, or Smart-seq scRNA-seq data
- Running downstream single-cell analysis (doublet removal, integration, annotation)
- Processing bulk RNA-seq with STAR, HISAT2, Salmon, or Kallisto
- Generating gene/transcript count matrices and QC reports
Spatial Omics Pipelines
Pipelines for spatial transcriptomics platforms including Visium, Xenium,
MERSCOPE, CosMX, and molecular cartography.
Skill file: nfcore_spatial.md
When to use:
- Processing 10x Visium or Visium HD data
- Analyzing Xenium in situ data with cell segmentation
- Running technology-agnostic spatial pipelines (sopa)
- Processing Resolve Bioscience Molecular Cartography data
Epigenomics Pipelines
Pipelines for chromatin accessibility, histone modification, protein-DNA
interaction, and DNA methylation profiling.
Skill file: nfcore_epigenomics.md
When to use:
- Processing ATAC-seq data (bulk)
- Analyzing ChIP-seq experiments with peak calling
- Running CUT&Run or CUT&Tag with spike-in normalization
- Processing bisulfite sequencing or TAPS methylation data
Variant Calling Pipeline (Sarek)
Germline and somatic variant detection from WGS, WES, or targeted
sequencing data with 16+ variant callers.
Skill file: nfcore_variant_calling.md
When to use:
- Detecting germline or somatic SNVs, indels, SVs, and CNVs
- Processing tumor/normal pairs or tumor-only samples
- Running multi-caller consensus variant analysis
- Annotating variants with SnpEff or VEP
Hi-C Chromatin Conformation Pipeline
Pipeline for processing Hi-C chromosome conformation capture data to study
3D genome organization: contact maps, TADs, and A/B compartments.
Skill file: nfcore_hic.md
When to use:
- Processing Hi-C data (digestion or DNase protocol)
- Generating multi-resolution contact maps (.cool/.mcool)
- Calling TADs and A/B compartments
- Studying 3D genome organization and chromatin interactions
Dynamic Pipeline Discovery (All 143+ Pipelines)
Meta-skill for dynamically discovering and using any nf-core pipeline,
including those not covered by the skill files above. Teaches the agent
how to fetch pipeline documentation, parameters, and samplesheet formats
on-the-fly from standardized nf-core URLs and schemas.
Skill file: nfcore_dynamic_discovery.md
When to use:
- User asks about a pipeline not covered in the detailed skill files above
- Exploring what pipelines are available for a specific data type
- Need to look up parameters or samplesheet format for any nf-core pipeline
- Pipeline has been updated and you need the latest information
[!TIP]
The detailed skill files above cover the most commonly used pipelines with
full parameter tables and examples. For all other pipelines, use the dynamic
discovery skill to fetch information on-the-fly from nf-co.re.
Using Skills
- Start with usage guide: Read
nfcore_usage.md for installation and configuration
- Select pipeline skill: Choose the skill matching your data type
- Pipeline not listed? Use
nfcore_dynamic_discovery.md to fetch docs on-the-fly
- Follow samplesheet format: Each pipeline requires a specific CSV samplesheet
- Test first: Always run with
-profile test,docker before real data
- Use
-resume: Re-run failed pipelines without recomputing successful steps
