Singularity Container Backend Setup

singularity-container-backend-setup

Summary

Configure and execute a Nextflow workflow using Singularity as the container backend for reproducible LC-HRMS metabolomics data processing on high-performance computing environments. This skill enables portable, containerized execution of MS-DIAL and MSFLO tools across HPC systems without Docker.

When to use

Your LC-HRMS metabolomics analysis must run on a high-performance computing cluster (e.g., HiPerGator, SLURM-managed systems) that lacks Docker support or prefers Singularity for security and portability. You have .mzML or .abf raw MS data files and need reproducible MS-DIAL → MSFLO processing across multiple compute nodes.

When NOT to use

• Your compute environment has Docker available and no security constraints against it; Docker provides faster image startup than Singularity.
• You are running on a local macOS or Linux workstation with sufficient disk space; the docker profile is simpler to configure for single-machine execution.
• Your raw data is already in a processed feature matrix or aligned peak table format; this skill targets raw .mzML/.abf ingestion only.

Inputs

• .mzML raw LC-HRMS data files
• .abf raw LC-HRMS data files (alternative format)
• msdial_params.txt configuration file
• msflo_params.ini configuration file
• ms1_lib.txt MS1 spectral library
• ms2_lib.msp MS2 spectral library

Outputs

• .tsv feature tables (MS-DIAL peak detection results)
• Aligned peak list (MS-DIAL chromatogram alignment output)
• Metabolite identification results (MSFLO annotated compounds)
• execution_report.html (workflow runtime and resource usage summary)
• execution_timeline.html (per-process execution timeline)

How to apply

Install Nextflow ≥22.10.0 and Singularity on your HPC system. Clone the Nextflow4MS-DIAL repository and place your .mzML input files in the data/raw_data/ directory. Configure MS-DIAL and MS-FLO parameter files (msdial_params.txt and msflo_params.ini) and MS1/MS2 spectral libraries (ms1_lib.txt and ms2_lib.msp) in the data/ folder. Execute the workflow using the singularity profile via nextflow run main.nf -profile singularity, which selects the Singularity executor and retrieves pre-built container images for MS-DIAL and MSFLO. Monitor execution via the generated execution_report.html and execution_timeline.html files. Validate completion by checking the results/ directory for .tsv-formatted MS-DIAL and MSFLO output files.

Related tools

• Nextflow (Workflow orchestration engine that manages containerized task execution and resource allocation across HPC environments) — https://www.nextflow.io/
• Singularity (Container runtime that isolates MS-DIAL and MSFLO tools with their dependencies and executes them on HPC clusters) — https://www.sylabs.io/guides/3.0/user-guide/
• MS-DIAL (Core metabolomics tool for untargeted peak detection, alignment, and deconvolution of LC-HRMS data)
• MSFLO (Post-processing tool for metabolite identification and annotation of MS-DIAL peak features)

Examples

nextflow run main.nf -profile singularity > logs/execution.log

Evaluation signals

• Workflow execution completes without containerization errors; check logs/execution.log for 'completed successfully' or absence of OCI/Singularity runtime exceptions.
• All expected output files are present in results/: .tsv feature tables, aligned peak list, and MSFLO annotations match the number of input .mzML files.
• execution_report.html and execution_timeline.html are generated and show non-zero CPU/memory usage and process completion times for MS-DIAL and MSFLO tasks.
• Output .tsv files are non-empty and contain numeric feature intensities, m/z values, retention times, and metabolite names (if annotated by MSFLO).
• Singularity container image pull/cache messages appear in execution logs, confirming image retrieval before task execution.

Limitations

• Singularity container images must be pre-built and hosted in a registry (e.g., Docker Hub, Singularity Hub) accessible from the HPC cluster; custom MS-DIAL or MSFLO versions require rebuilding the container.
• MS-DIAL and MSFLO version information is not explicitly specified in the container tags; reproducibility depends on pinning image digests, not just tags, which the current configuration does not enforce.
• HPC configuration (CPU, memory, wall-time limits) is environment-specific; the provided HiPerGator.config example may not transfer directly to other SLURM or non-SLURM schedulers without manual adjustment.
• File naming must avoid special characters (underscores are safe); the workflow does not sanitize input filenames, leading to silent failures or skipped files with problematic names.
• Parameter validation and MS1/MS2 library consistency are not automatically checked; malformed msdial_params.txt or missing/empty library files will cause cryptic downstream MS-DIAL failures.

Evidence

• [readme] Both Docker and Singularity (for high-performance computing) are supported: "Both Docker and Singularity (for high-performance computing) are supported"
• [other] Configure Singularity as container backend for HPC: "Configure the Nextflow workflow to use Singularity as the container backend (as an alternative to Docker)."
• [readme] Execute with Singularity profile: "Use the docker profile for local execution and the singularity profile for high-performance computing environments"
• [readme] Validate outputs in results directory: "Example outputs are stored in the results folder. The file extensions for produced .msdial files have been changed to .tsv"
• [readme] Tested on HiPerGator HPC environment: "HiPerGator, the University of Florida public research computing environment, running Red Hat Enterprise Linux 8.8"