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fazal-contra edited this page Jan 20, 2026 · 1 revision

Getting Started

This guide will help you set up and run your first ELDEN-RING pipeline.

Prerequisites

Software Requirements

Software Version Purpose
Nextflow 21.10.0+ Pipeline orchestration
Singularity/Apptainer 3.0+ Container runtime
NVIDIA Driver Compatible with CUDA GPU acceleration

Hardware Requirements

  • CPU: Multi-core processor (recommended: 16+ cores)
  • RAM: 64GB+ recommended for large datasets
  • GPU: NVIDIA GPU with CUDA support (for peasoup searches)
  • Storage: Sufficient space for input data and outputs

Installation

1. Install Nextflow

# Using curl
curl -s https://get.nextflow.io | bash

# Or using conda
conda install -c bioconda nextflow

2. Clone the Repository

git clone https://github.com/your-org/elden-ring.git
cd elden-ring

3. Verify Container Access

Ensure Singularity containers are accessible. The pipeline uses pre-built containers for:

  • peasoup - GPU periodicity search
  • pulsarx - Candidate folding
  • presto - Pulsar utilities
  • pics_classifier - ML classification
  • rfi_mitigation - RFI filtering
  • filtools - Filterbank tools

Quick Start

Step 1: Setup Project Directory

nextflow run elden.nf -entry setup_basedir --basedir /path/to/your/project

This creates the necessary directory structure:

/path/to/your/project/
├── params.config
├── inputfile.txt
├── dada_input.csv (if applicable)
└── known_pulsars.csv

Step 2: Generate Input File

Use the helper script to generate the input CSV:

bash generate_inputfile.sh \
    --cluster NGC6401 \
    --ra 17:38:36.83 \
    --dec -23:54:33.9 \
    --utc 2025-09-14T16:01:33 \
    --cdm "47.0 101.0" \
    /path/to/filterbank/data/

Or manually create inputfile.txt:

pointing,cluster,beam_name,beam_id,utc_start,ra,dec,fits_files,cdm
0,NGC6401,cfbf00003,3,2025-09-14T16:01:33.9,17:38:36.53,-23:54:34.6,/data/beam3.fil,47.0

Step 3: Configure Parameters

Edit params.config in your project directory:

params {
    basedir = "/path/to/your/project"
    runID = "search_v1"
    files_list = "inputfile.txt"
    telescope = "effelsberg"

    ddplan {
        dm_start = 85
        dm_end = 95
        dm_step = 0.1
    }

    peasoup {
        segments = [1, 2, 4]
        acc_start = -50
        acc_end = 50
        min_snr = 7.0
    }
}

Step 4: Validate Inputs

Before running the full pipeline, validate your configuration:

nextflow run elden.nf -entry validate_inputs \
    -c params.config \
    --basedir /path/to/your/project

Step 5: Run the Pipeline

# Full pipeline with local profile
nextflow run elden.nf -entry full \
    -profile local \
    -c params.config \
    --runID search_v1

# Or with SLURM cluster profile
nextflow run elden.nf -entry full \
    -profile hercules \
    -c params.config \
    --runID search_v1 \
    -resume

Common Entry Points

Entry Point Use Case
-entry full Complete pipeline from raw data to classified candidates
-entry run_dada_search Process DADA baseband files
-entry run_rfi_clean RFI cleaning only
-entry run_search_fold Search and fold pre-cleaned files
-entry fold_par Fold with known pulsar ephemeris

Resuming Interrupted Runs

Nextflow supports resuming interrupted pipelines:

nextflow run elden.nf -entry full \
    -profile hercules \
    -c params.config \
    -resume

The -resume flag uses cached results from previous runs.

Next Steps

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