القائمة
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.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Debug Airflow DAGs locally using dag.test() in an IDE or command line with pdb. Use when debugging DAG execution, task failures, import errors, or testing DAGs without deploying to Airflow.
Comprehensive guide for testing Apache Airflow DAGs including unit tests, integration tests, load tests, mocking, and best practices for Airflow 3 repositories.
Workflow and best practices for writing Apache Airflow 3 DAGs. Use when the user wants to write a new DAG, pipeline code, or asks about DAG patterns and conventions.
Guide for analyzing pipeline output and debugging Nextflow workflows. Use this when you need to inspect channel contents, trace process execution, or analyze intermediate files.
Research and recommend the best bioinformatics tool for a specific task. Use this when you need to select appropriate tools for bioinformatics analysis based on requirements, performance, integration, and community support.
Guide for creating Mermaid diagrams (.mmd files) from Nextflow pipeline code. Use this when asked to create workflow diagrams from subworkflows or main.nf scripts.
| 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