Update nf-core Modules

Update modules installed from nf-core/modules to their latest versions.

Quick Commands

bash

# Check for updates (preview only)
conda run -n nf-core nf-core modules update --preview

# Update specific module
conda run -n nf-core nf-core modules update fastqc

# Update all modules
conda run -n nf-core nf-core modules update --all

# Update to specific commit
conda run -n nf-core nf-core modules update fastqc --sha abc123

# Force update (even if up-to-date)
conda run -n nf-core nf-core modules update fastqc --force

# Save diff instead of applying
conda run -n nf-core nf-core modules update fastqc --save-diff updates.patch

Process

•Preview Updates: Run with --preview to see available updates
•Review Changes: Check what will change
•Update Modules: Apply updates
•Handle Patches: Re-apply any local patches
•Test: Run tests to verify functionality
•Commit: Commit updated modules

Update Modes

Preview Mode

bash

conda run -n nf-core nf-core modules update --preview

Shows what would be updated without making changes.

Interactive Update

bash

conda run -n nf-core nf-core modules update fastqc --prompt

Prompts for version selection.

Silent Update

bash

conda run -n nf-core nf-core modules update --all

Updates all modules to latest without prompts.

Handling Local Modifications

If you've modified installed modules:

Option 1: Create Patch Before Update

bash

# Create patch from modifications
conda run -n nf-core nf-core modules patch fastqc

# Update module (patch auto-applied)
conda run -n nf-core nf-core modules update fastqc

Option 2: Save Diff

bash

# Save update as diff file
conda run -n nf-core nf-core modules update fastqc --save-diff fastqc.patch

# Review and apply manually
git apply fastqc.patch

Option 3: Force Update

bash

# Overwrite local changes
conda run -n nf-core nf-core modules update fastqc --force

# Re-apply custom changes manually

Module Versioning

Modules are tracked in modules.json:

json

{
  "repos": {
    "https://github.com/nf-core/modules.git": {
      "modules": {
        "nf-core": {
          "fastqc": {
            "branch": "master",
            "git_sha": "abc123def456...",
            "installed_by": ["modules"]
          }
        }
      }
    }
  }
}

Checking Installed Versions

bash

# List all installed modules with versions
conda run -n nf-core nf-core modules list local

# Get info about specific module
conda run -n nf-core nf-core modules info fastqc

Update Workflow

Single Module Update

bash

# 1. Check current version
conda run -n nf-core nf-core modules info fastqc

# 2. Preview update
conda run -n nf-core nf-core modules update fastqc --preview

# 3. Apply update
conda run -n nf-core nf-core modules update fastqc

# 4. Test
conda run -n nf-core nf-test test modules/nf-core/fastqc/

# 5. Commit
git add modules/nf-core/fastqc/ modules.json
git commit -m "Update fastqc module"

Bulk Update

bash

# 1. Preview all updates
conda run -n nf-core nf-core modules update --all --preview

# 2. Apply all updates
conda run -n nf-core nf-core modules update --all

# 3. Run all tests
conda run -n nf-core nf-test test

# 4. Commit
git add modules/ modules.json
git commit -m "Update all nf-core modules"

Troubleshooting

Merge Conflicts

If patch application fails:

bash

# Remove patch
rm modules/nf-core/tool/.nf-core-patch.yaml

# Force update
conda run -n nf-core nf-core modules update tool --force

# Re-apply changes manually and create new patch
conda run -n nf-core nf-core modules patch tool

Module Not Found

bash

# Refresh module list
conda run -n nf-core nf-core modules list remote --update

Version Pinning

To pin a module to specific version:

bash

# Install specific version
conda run -n nf-core nf-core modules install fastqc --sha specific_commit

# Don't update this module
# (manually exclude from --all updates)

Best Practices

•Update regularly: Keep modules current for bug fixes and features
•Test after updates: Run nf-test suite
•Review changelogs: Check nf-core/modules for breaking changes
•Use patches: Don't modify modules directly; use patch system
•Commit separately: Update modules in dedicated commits