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Guide for interacting with nf-core modules and subworkflows. Use this when you need to discover, view, install, or update nf-core modules/subworkflows in your pipeline.
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| name | nf-core-modules-subworkflows |
| description | Guide for interacting with nf-core modules and subworkflows. Use this when you need to discover, view, install, or update nf-core modules/subworkflows in your pipeline. |
This guide covers how to discover, view, install, and update nf-core modules and subworkflows in your pipeline.
nf-core is installed via pyproject.toml.
CRITICAL: use source .venv/bin/activate to activate the virtual environment before running nf-core commands, to ensure you are using the correct version of nf-core and its dependencies.
To see all modules available in the nf-core repository:
# List all remote modules
nf-core modules list remote
# Search for specific module by keyword (e.g., "fastq")
nf-core modules list remote fastq
Always try to search for a keyword as the raw list of modules can be overwhelming. The search will match both module names and descriptions.
To see all subworkflows available in the nf-core repository:
# List all remote subworkflows
nf-core subworkflows list remote
# Search for specific subworkflow by keyword (e.g., "bam")
nf-core subworkflows list remote bam
To see what's already installed in your pipeline:
# List locally installed modules
nf-core modules list local
# List locally installed subworkflows
nf-core subworkflows list local
# Specify a different pipeline directory
nf-core modules list local --dir /path/to/pipeline
Get detailed information about a specific module:
# View module documentation and metadata
nf-core modules info <module_name>
# Examples:
nf-core modules info fastqc
nf-core modules info samtools/sort
This displays:
Get detailed information about a specific subworkflow:
# View subworkflow documentation
nf-core subworkflows info <subworkflow_name>
# Example:
nf-core subworkflows info bam_rseqc
There are several ways to view the actual source code:
Modules:
https://github.com/nf-core/modules/tree/master/modules/nf-core/<module_name>Subworkflows:
https://github.com/nf-core/modules/tree/master/subworkflows/nf-core/<subworkflow_name>Visit https://nf-co.re/modules to:
Once installed, modules and subworkflows are available locally:
# Modules are installed to:
./modules/nf-core/<module_name>/
# Subworkflows are installed to:
./subworkflows/nf-core/<subworkflow_name>/
View them with your editor or terminal:
# View a module's main script
cat modules/nf-core/fastqc/main.nf
# View a subworkflow
cat subworkflows/nf-core/bam_rseqc/main.nf
# Interactive selection
nf-core modules install
# Install specific module directly
nf-core modules install <module_name>
# Examples:
nf-core modules install fastqc
nf-core modules install samtools/sort
# Install from a different directory
nf-core modules install fastqc --dir /path/to/pipeline
Installation Options:
--force: Overwrite previously installed version--prompt: Interactively select the module version--sha <commit_sha>: Install from a specific commit# Install specific version by SHA
nf-core modules install fastqc --sha abc123def456
# Force reinstall
nf-core modules install fastqc --force
# Interactive selection
nf-core subworkflows install
# Install specific subworkflow directly
nf-core subworkflows install <subworkflow_name>
# Example:
nf-core subworkflows install bam_rseqc
# Install from a different directory
nf-core subworkflows install bam_rseqc --dir /path/to/pipeline
Installation Options:
--dir: Specify pipeline directory (default: current directory)--force: Overwrite previously installed version--prompt: Interactively select version--sha <commit_sha>: Install from specific commit# Interactive update (select which module to update)
nf-core modules update
# Update specific module
nf-core modules update <module_name>
# Examples:
nf-core modules update fastqc
nf-core modules update samtools/sort
# Update all modules at once
nf-core modules update --all --no-preview
Update Options:
--all: Update all modules in the pipeline--force: Reinstall even if up to date--prompt: Select version interactively--sha <commit_sha>: Update to specific commit--preview / --no-preview: Show/hide diff before updating--save-diff <filename>: Save diffs to file for review# Update with preview of changes
nf-core modules update fastqc --preview
# Update all modules without preview
nf-core modules update --all --no-preview
# Save diffs for manual review
nf-core modules update fastqc --save-diff fastqc.diff
git apply fastqc.diff # Apply later if desired
# Interactive update
nf-core subworkflows update
# Update specific subworkflow
nf-core subworkflows update <subworkflow_name>
# Example:
nf-core subworkflows update bam_rseqc
# Update all subworkflows at once
nf-core subworkflows update --all --no-preview
Update Options:
--dir: Specify pipeline directory--all: Update all subworkflows--force: Reinstall even if up to date--prompt: Select version interactively--sha <commit_sha>: Update to specific commit--preview / --no-preview: Show/hide diff before updating--save-diff <filename>: Save diffs to file--update-deps: Automatically update all dependencies# Update with dependency check
nf-core subworkflows update bam_rseqc --update-deps
# Preview changes before updating
nf-core subworkflows update bam_rseqc --preview
| Task | Modules Command | Subworkflows Command |
|---|---|---|
| List remote | nf-core modules list remote | nf-core subworkflows list remote |
| List local | nf-core modules list local | nf-core subworkflows list local |
| Get info | nf-core modules info <name> | nf-core subworkflows info <name> |
| Install | nf-core modules install <name> | nf-core subworkflows install <name> |
| Update | nf-core modules update <name> | nf-core subworkflows update <name> |
| Update all | nf-core modules update --all | nf-core subworkflows update --all |
# 1. Search for the module
nf-core modules list remote | grep samtools
# 2. Get information about it
nf-core modules info samtools/sort
# 3. View code on GitHub (in browser)
# Navigate to: https://github.com/nf-core/modules/tree/master/modules/nf-core/samtools/sort
# 4. Install the module
nf-core modules install samtools/sort
# 5. Include in your workflow (edit main.nf or relevant .nf file)
# include { SAMTOOLS_SORT } from './modules/nf-core/samtools/sort/main'
--preview flag when updating to review changes.nf-core.yml for production pipelinesLast updated: February 2026 For the most current information, visit https://nf-co.re/docs/nf-core-tools