nf-core Module Installation

Install pre-built modules from the nf-core/modules repository into your pipeline.

Quick Commands

bash

# List all available remote modules
conda run -n nf-core nf-core modules list remote

# Search for a specific module
conda run -n nf-core nf-core modules list remote | grep -i "tool_name"

# List installed modules in current pipeline
conda run -n nf-core nf-core modules list local

# Install a module
conda run -n nf-core nf-core modules install <tool/subtool>

# Install specific version
conda run -n nf-core nf-core modules install <module> --sha <commit_sha>

# Force reinstall
conda run -n nf-core nf-core modules install <module> --force

# Get module info
conda run -n nf-core nf-core modules info <module>

Process

•Identify Module: Search for the module by tool name
•Check Availability: Verify module exists in nf-core/modules
•Review Info: Check module documentation with nf-core modules info
•Install: Run the install command
•Integrate: Add the module to your workflow

Module Naming Convention

Modules use the format tool/subtool:

•fastqc - Single tool
•bwa/mem - Tool with subtool
•samtools/sort - Tool with subtool
•samtools/index - Same tool, different subtool

Installation Location

Modules are installed to:

code

modules/nf-core/<tool>/<subtool>/
├── main.nf          # Process definition
├── meta.yml         # Metadata (inputs, outputs, params)
└── tests/
    ├── main.nf.test # nf-test tests
    └── main.nf.test.snap # Test snapshots

Integration Example

After installing a module like fastqc:

nextflow

// In your workflow file
include { FASTQC } from '../modules/nf-core/fastqc/main'

workflow MY_WORKFLOW {
    take:
    reads  // channel: [ val(meta), path(reads) ]

    main:
    FASTQC ( reads )

    emit:
    zip   = FASTQC.out.zip   // channel: [ val(meta), path(zip) ]
    html  = FASTQC.out.html  // channel: [ val(meta), path(html) ]
}

Using ext.args for Tool Arguments

Pass additional arguments to tools via ext.args in your config:

nextflow

// conf/modules.config
process {
    withName: FASTQC {
        ext.args = '--quiet'
        publishDir = [
            path: { "${params.outdir}/fastqc" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
        ]
    }
}

Popular Modules

Module	Purpose
`fastqc`	Read quality control
`multiqc`	Report aggregation
`trimgalore`	Adapter and quality trimming
`bwa/mem`	Read alignment
`bwa/mem2`	Faster read alignment
`samtools/sort`	BAM sorting
`samtools/index`	BAM indexing
`samtools/stats`	BAM statistics
`bcftools/call`	Variant calling
`gatk4/markduplicates`	Duplicate marking

Troubleshooting

Module Not Found

bash

# Update modules list
conda run -n nf-core nf-core modules list remote --update

# Check exact name
conda run -n nf-core nf-core modules list remote | grep -i "partial_name"

Version Conflicts

bash

# Check installed version
conda run -n nf-core nf-core modules list local

# Update to latest
conda run -n nf-core nf-core modules update <module>

# Install specific version
conda run -n nf-core nf-core modules install <module> --sha <commit>