nf-core Tools

The nf-core tools provide access to 1630+ pre-built, standardized Nextflow bioinformatics modules and pipelines. These tools help discover modules for specific tasks, get detailed usage information, and receive recommendations for analysis pipelines based on your data type.

Available tools

search_nfcore_module

Search nf-core modules using natural language queries. Find modules for tasks like alignment, variant calling, quality control, assembly, and annotation.

Example prompts:

• "Find nf-core modules for quality control of sequencing data"
• "Search for alignment modules that support paired-end reads"
• "What modules are available for variant calling?"
• "Find modules for RNA-seq quantification"
• "Search for tools that can trim adapters from FASTQ files"

describe_nfcore_module

Get comprehensive metadata for a specific module including input/output schemas, command templates, configuration examples, and AI execution guidance.

Example prompts:

• "Describe the nf-core/fastqc module"
• "Show me how to use the bwa/mem module"
• "What are the inputs and outputs for samtools/sort?"
• "Give me the Nextflow command to run the multiqc module"
• "How do I configure the star/align module for my analysis?"

nfcore_suggest_analysis

Suggest appropriate nf-core pipelines and reference genomes based on library strategy and organism. Maps sequencing assay types to recommended analysis workflows.

Supported library strategies:

• RNA-Seq, mRNA-Seq → nf-core/rnaseq
• WGS, WXS → nf-core/sarek
• ATAC-Seq → nf-core/atacseq
• ChIP-Seq → nf-core/chipseq
• Bisulfite-Seq → nf-core/methylseq
• miRNA-Seq → nf-core/smrnaseq
• Amplicon → nf-core/ampliseq
• Hi-C → nf-core/hic

Supported organisms (with genome builds):

• Homo sapiens → GRCh38
• Mus musculus → GRCm39
• Rattus norvegicus → Rnor_6.0
• Danio rerio → GRCz11
• Drosophila melanogaster → BDGP6
• Arabidopsis thaliana → TAIR10
• And many more...

Example prompts:

• "What pipeline should I use for human RNA-seq data?"
• "Suggest an analysis pipeline for mouse ATAC-seq"
• "What's the recommended genome for Homo sapiens?"
• "I have WGS data from zebrafish, what should I use?"
• "Recommend a pipeline for ChIP-seq analysis of mouse samples"

Typical workflow

1. Search for modules using natural language with search_nfcore_module
2. Describe specific modules to understand inputs, outputs, and usage with describe_nfcore_module
3. Suggest the best pipeline and genome for your data type with nfcore_suggest_analysis
4. Execute the recommended pipeline with Nextflow

Example session

User: I have paired-end RNA-seq data from human liver samples. What should I use to analyze it?

AI: [Uses nfcore_suggest_analysis]
    Recommended pipeline: nf-core/rnaseq
    Pipeline URL: https://nf-co.re/rnaseq
    Reference genome: GRCh38
    iGenomes path: s3://ngi-igenomes/igenomes/GRCh38

User: What modules does rnaseq use for quality control?

AI: [Uses search_nfcore_module with "quality control RNA-seq"]
    Found relevant modules:
    1. nf-core/fastqc - QC checks on sequencing data
    2. nf-core/multiqc - Aggregate QC reports
    3. nf-core/trimgalore - Adapter and quality trimming

User: Tell me more about fastqc

AI: [Uses describe_nfcore_module for nf-core/fastqc]
    Module: nf-core/fastqc
    Description: Run FastQC quality control checks on sequencing data

    Inputs:
    - reads: FASTQ files (*.fastq.gz)

    Outputs:
    - html: FastQC HTML report
    - zip: FastQC data archive

    Nextflow command:
    nextflow run nf-core/fastqc \
      --input samplesheet.csv \
      --outdir results \
      -profile docker

Pipeline mapping reference

Library strategy	nf-core Pipeline	Description
RNA-Seq	rnaseq	RNA sequencing analysis
WGS/WXS	sarek	Variant calling for germline/somatic
ATAC-Seq	atacseq	Chromatin accessibility
ChIP-Seq	chipseq	Protein-DNA binding
Bisulfite-Seq	methylseq	DNA methylation
miRNA-Seq	smrnaseq	Small RNA analysis
Amplicon	ampliseq	Amplicon sequencing
Hi-C	hic	Chromosome conformation

Genome reference

Organism	Common name	Genome build
Homo sapiens	Human	GRCh38
Mus musculus	Mouse	GRCm39
Rattus norvegicus	Rat	Rnor_6.0
Danio rerio	Zebrafish	GRCz11
Drosophila melanogaster	Fruit fly	BDGP6
Caenorhabditis elegans	Worm	WBcel235
Saccharomyces cerevisiae	Yeast	R64-1-1
Arabidopsis thaliana	Arabidopsis	TAIR10