Add workflow for metagenomic taxonomic community profiling

[bebatut]

ping @Minamehr

FOR CONTRIBUTOR:

• I have read the Adding workflows guidelines
• License permits unrestricted use (educational + commercial)
• Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

• .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
• Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
• In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
• In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
• In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
• Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
• Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
• Changelog contains appropriate entries
• Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

[Minamehr]

Thanks a lot, Bérénice, really appreciate the improvements and cleanup.

[Copilot]

Pull request overview

This PR adds a new workflow for metagenomic taxonomic community profiling to the IWC. The workflow performs taxonomic profiling on quality-controlled metagenomic reads using multiple state-of-the-art tools (Kraken2/Bracken, MetaPhlAn, and Sylph), standardizes the outputs using TaxPasta, and generates visualizations with Krona and MultiQC.

Changes:

• Addition of a new workflow with comprehensive taxonomic profiling capabilities
• Implementation of multiple profiling approaches (k-mer and marker-based)
• Standardization and visualization of results across tools
• Support for both single and multiple sample processing

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
metagenomics-taxonomic-community-profiling.ga	Main workflow file implementing taxonomic profiling with three tools, standardization, and visualization steps
metagenomics-taxonomic-community-profiling-tests.yml	Test definitions for 1-sample and 2-sample scenarios with comprehensive output validation
README.md	Documentation explaining workflow purpose, inputs, processing steps, and expected outputs
CHANGELOG.md	Version history documenting initial release
.dockstore.yml	Dockstore configuration with workflow metadata and author information

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	0
Passed	0
Error	0
Failure	0
Skipped	0