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How this repo is used currently

In each nf-core config or pipeline, these lines are included. So basically, nf-core custom.config and the pipeline rnaseq.config will get pulled in.

// Load nf-core custom profiles from different institutions

// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
// Load nf-core/rnaseq custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

// Load nf-core/rnaseq custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/rnaseq.config" : "/dev/null"

New Directory Structure (2024)

We've reorganized cluster configurations to improve maintainability and co-locate related files. The new structure follows this pattern:

Structure Overview

conf/<cluster>/
├── nextflow.config                    # Main cluster configuration
├── README.md                         # Cluster documentation and usage
└── pipelines/                        # Pipeline-specific configurations
    ├── <pipeline1>/
    │   ├── nextflow.config           # Pipeline-specific config
    │   └── README.md                 # Pipeline-specific docs
    └── <pipeline2>/
        ├── nextflow.config
        └── README.md

Examples

UPPMAX (complex cluster with pipeline-specific configs)

conf/uppmax/
├── nextflow.config                    # Main UPPMAX configuration
├── README.md                         # UPPMAX usage guide
└── pipelines/
    ├── ampliseq/
    │   ├── nextflow.config           # AmplicSeq-specific UPPMAX config
    │   └── README.md                 # AmplicSeq on UPPMAX docs
    └── sarek/
        ├── nextflow.config           # Sarek-specific UPPMAX config
        └── README.md                 # Sarek on UPPMAX docs

Sanger (simple cluster with just main config)

conf/sanger/
├── nextflow.config                    # Main Sanger configuration
└── README.md                         # Sanger usage guide (if exists)

Migration Process

Automated Migration

Use the provided automation script to reorganize existing clusters:

./bin/reorganize-cluster.sh <cluster_name>

This script:

  1. Creates the cluster directory if it doesn't exist
  2. Moves conf/cluster.config → conf/cluster/nextflow.config
  3. Renames pipeline/ → pipelines/ (if exists)
  4. Moves pipeline configs from conf/pipeline/*/cluster.config
  5. Moves pipeline docs from docs/pipeline/*/cluster.md
  6. Updates nfcore_custom.config with the new path
  7. Cleans up duplicate files

Manual Steps (if needed)

  1. Create directory: mkdir conf/<cluster>
  2. Move main config: mv conf/<cluster>.config conf/<cluster>/nextflow.config
  3. Move pipeline configs: mv conf/pipeline/<pipeline>/<cluster>.config conf/<cluster>/pipelines/<pipeline>/nextflow.config
  4. Move documentation: mv docs/pipeline/<pipeline>/<cluster>.md conf/<cluster>/pipelines/<pipeline>/README.md
  5. Update registry: Edit nfcore_custom.config to point to conf/<cluster>/nextflow.config

Benefits

  • Co-location: All cluster-related files are in one place
  • Consistent naming: nextflow.config and README.md everywhere
  • Better discoverability: Easier for maintainers to find cluster-specific files
  • Reduced duplication: Single source of truth for each cluster configuration
  • Improved maintainability: Clear separation between general and pipeline-specific configs

Registry Update Required

When moving cluster configs, always update nfcore_custom.config:

profiles {
    cluster_name {
-       includeConfig "${params.custom_config_base}/conf/cluster_name.config"
+       includeConfig "${params.custom_config_base}/conf/cluster_name/nextflow.config"
    }
}

This is automatically handled by the reorganization script.