MetaPathways 4.0.0: Nextflow local/Slurm workflows, PGDB builds and explorer

[RyloByte]

MetaPathways 4.0.0 runs complete multi-sample annotation, read abundance, population/community PGDB inference and reporting through Nextflow on a local server or Slurm. Existing module commands remain available, with explicit resource controls and shared multi-sample input discovery/manifests.

The update adds licensed Pathway Tools container and MetaCyc preparation, sequence-backed PGDB inputs, reaction compatibility screening, compact storage with node-local execution, and connected report/explorer tables. It also fixes read-pair/BAM selection, checkpoints, annotation-associated taxonomy, rRNA counters and zero-pathway PGDB exports.

Release metadata and installation examples now use 4.0.0. Development integrates through dev; main is the production/default branch. Conda and Quay publication remain manually selected after installed-package/container validation, with GitHub/Zenodo publication separate.

Validation of the release-preparation revision:

• 170 runtime tests and 20 release-control tests passed.
• Strict documentation build, rendered links/anchors and citation schema passed.
• Source distribution and Linux/Python 3.11 wheel built successfully.
• Installed wheel verified outside the checkout: CLI/version, workflow assets, bundled test preparation, MAGSplitter and Camelot.
• The completed corrected HPC benchmark is retained separately under its actual 3.5.2 version; it is not relabelled as a 4.0.0 run.
• Final committed Conda and Docker/Apptainer artifacts will be validated by the nonpublishing Release workflow before registry publication.

[read-the-docs-community]

Documentation build overview

📚 HallamLab-MetaPathways | 🛠️ Build #35050730 | 📁 Comparing 42da2b1 against latest (9d6990a)

  🔍 Preview build  

26 files changed · + 3 added · ± 23 modified

+ Added

• WORKFLOW_STYLE.html
• test-bundle.html
• test.html

± Modified

• annotation.html
• benchmarking.html
• cami-references.html
• cli-reference.html
• commands.html
• containers.html
• detailed-workflow.html
• documentation.html
• execution.html
• getting-started.html
• and 13 more...