Docker container orchestration

docker-container-orchestration

Summary

Execute reproducible LC-HRMS metabolomics workflows using Docker containerization of MS-DIAL and MSFLO tools via Nextflow, enabling portable and isolated processing of .mzML mass spectrometry data across heterogeneous computational environments.

When to use

When you have .mzML or .abf LC-HRMS raw data files that require MS-DIAL-based feature detection, chromatogram alignment, and metabolite identification, and you need to ensure reproducibility across local machines, cloud, and HPC systems without manual tool installation and dependency management.

When NOT to use

• Input data is already processed into a feature table or peak matrix — use this skill only when starting from raw .mzML or .abf chromatography-mass spectrometry files.
• Your computing environment has strict restrictions on Docker daemon access or does not support container runtimes (in such cases, use the Singularity profile instead).
• You require real-time interactive parameter tuning during processing; Docker containerization assumes pre-configured static parameters in configuration files.

Inputs

• .mzML files (Liquid Chromatography-High Resolution Mass Spectrometry raw data)
• .abf files (alternative LC-HRMS format)
• MS-DIAL parameter configuration file (msdial_params.txt)
• MS-FLO parameter configuration file (msflo_params.ini)
• MS1 spectral library (ms1_lib.txt)
• MS2 spectral library (ms2_lib.msp)

Outputs

• Feature detection tables (.tsv files converted from .msdial)
• Aligned data matrices (MS-DIAL aligned features)
• Processed metabolite annotations (MS-FLO results)
• Execution report (execution_report.html)
• Execution timeline (execution_timeline.html)
• Workflow logs (logs/execution.log)

How to apply

Install Nextflow ≥22.10.0 and Docker, then clone the Nextflow4MS-DIAL repository. Prepare your .mzML metabolomics dataset and place it in the data/raw_data/ directory. Configure MS-DIAL parameters in msdial_params.txt and MS-FLO parameters in msflo_params.ini (example files are provided in functional_test/sample_data/), and add MS1 and MS2 spectral libraries as ms1_lib.txt and ms2_lib.msp. Execute the workflow with the Docker profile: nextflow run main.nf -profile docker. The containerized MS-DIAL and MSFLO tools run inside isolated Docker images, eliminating version conflicts and platform-specific issues. Monitor execution via execution_report.html (runtime and resource usage) and execution_timeline.html (process timeline) to verify all pipeline stages complete without error.

Related tools

• Nextflow (Workflow orchestration engine that manages containerized tool execution, resource allocation, and job scheduling across local and distributed computational environments.) — https://www.nextflow.io/
• MS-DIAL (Containerized bioinformatics tool for untargeted LC-HRMS metabolomics data processing, including peak detection, deconvolution, and feature alignment.)
• MSFLO (Containerized post-processing tool for MS-DIAL output that performs metabolite annotation and library matching.)
• Docker (Container runtime that packages MS-DIAL and MSFLO tools with all dependencies into isolated, reproducible execution environments.) — https://docs.docker.com/engine/installation/
• Singularity (Alternative container runtime supported by the workflow for high-performance computing environments where Docker is unavailable.) — https://www.sylabs.io/guides/3.0/user-guide/

Examples

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

Evaluation signals

• All workflow stages complete without errors in logs/execution.log; no process reports failure status.
• Expected output files are present and non-empty in the results directory: feature detection tables (converted .tsv files from .msdial), aligned data matrices, and metabolite annotations.
• Execution report (execution_report.html) displays successful completion status, total runtime, and per-process resource utilization within expected ranges.
• Workflow produces consistent feature tables and aligned data across repeated runs with identical input parameters (reproducibility validation).
• Container images for MS-DIAL and MSFLO are successfully pulled and executed without registry or Docker daemon errors (verify in execution logs).

Limitations

• File names must not contain special characters; only underscores are safe (spaces, dashes, and other symbols cause unexpected errors).
• Input .mzML and .abf files must be converted from other raw mass spectrometry formats using external tools (ProteoWizard msConvert or Reifycs Abf Converter); the workflow does not perform format conversion.
• MS-DIAL and MSFLO tool versions are not explicitly specified in the workflow configuration; no version pinning or compatibility information is provided, which may affect reproducibility across software updates.
• The workflow has been validated only on macOS 13.5.1 (2.6 GHz 6-Core Intel Core i7, 16 GB memory) and Red Hat Enterprise Linux 8.8 (HiPerGator HPC); behavior on other operating systems or resource-constrained environments is untested.
• No explicit discussion of Docker image pull failures, network connectivity issues, or disk space requirements for containerized execution is provided.

Evidence

• [readme] A reproducible Nextflow workflow for LC-HRMS metabolomics data processing: "A reproducible Nextflow workflow for LC-HRMS metabolomics data processing with MS-DIAL."
• [readme] Containerized MS-DIAL and MSFLO workflow with Docker support: "processing .mzML LC-MS metabolomics data with containerized workflow MS-DIAL -> MSFLO"
• [readme] Docker and Singularity container support: "Both Docker and Singularity (for high-performance computing) are supported"
• [readme] Nextflow version requirement and Java dependency: "Install Java 11 or later. The workflow was developed with Java 11.0.8. Install Nextflow."
• [readme] Configuration and library file setup: "Add the MS-DIAL and MS-FLO configuration files to the data/ folder and name them msdial_params.txt and msflo_params.ini. Example configuration files are available in"
• [readme] Execution command with Docker profile: "nextflow run main.nf -profile docker > logs/execution.log"
• [readme] Execution monitoring via report files: "execution_report.html summarizes workflow runtime and computational resource usage. execution_timeline.html shows the execution timeline for each process."
• [readme] File naming restrictions for workflow execution: "To avoid unexpected errors, do not use special characters in file names. Underscores are safe to use."
• [readme] Platform and hardware testing scope: "It supports macOS and Linux and has been tested successfully on: macOS 13.5.1 with a 2.6 GHz 6-Core Intel Core i7 processor and 16 GB memory. HiPerGator, the University of Florida public research"
• [readme] Input data format requirements: "The workflow accepts .mzML and .abf files."