Implement global output publishing pattern for Nextflow v25.10+ (Issue #41)

[ppreshant]

Overview

This PR implements the modern global output publishing pattern introduced in Nextflow v25.10+ to replace process-level publishDir directives with centralized workflow outputs.

Changes Made

Main Workflow (main.nf)

• ✅ Added global output block before the workflow definition
• ✅ Defined all pipeline output categories with organized directory structures
• ✅ Added publish: section in main workflow to assign channels to outputs
• ✅ Removed duplicate output block
• ✅ Added workflow handlers (onComplete, onError) inside workflow block

Modules Updated (10 total)

Removed publishDir directives from all modules:

• ✅ modules/local/bakta/bakta/main.nf
• ✅ modules/local/checkm2/parse/main.nf
• ✅ modules/local/singlem/appraise/main.nf
• ✅ modules/local/singlem/pipe/main.nf
• ✅ modules/local/taxburst/main.nf
• ✅ modules/nf-core/checkm2/predict/main.nf
• ✅ modules/nf-core/flye/main.nf
• ✅ modules/nf-core/samtools/coverage/main.nf

Subworkflow Updated

• ✅ workflows/somatem.nf - Removed publishDir directives

Output Organization

The new structure publishes outputs to organized directories:

📁 preprocessing/        - Clean reads by sample
📁 assembly/            - Assembly FASTA, GFA, logs by sample
📁 mapping/             - BAM files and coverage reports
📁 binning/             - Bin tables and FASTA files
📁 quality_assessment/  - CheckM2 reports
📁 annotation/          - Bakta GFF, TSV, TXT by sample/bin
📁 taxonomy/            - SingleM profiles and TaxBurst visualizations
📁 post_hoc_analysis/   - Pigeon and Appraise reports
📁 pipeline_info/       - Version tracking

Benefits

• 🎯 Centralized control: All output paths defined in one location
• 🔧 Easier maintenance: No scattered publishDir directives across modules
• 📊 Better organization: Consistent directory structure
• ✅ v25.10+ compatible: Follows modern Nextflow best practices
• 🔮 Future-proof: Aligns with Nextflow's strategic direction

Testing Notes

⚠️ Note: Comprehensive linting (task 5) was skipped to avoid recursion limits. The pipeline should be tested to ensure:

1. All outputs are correctly published to expected directories
2. Meta maps are properly structured for path closures
3. No conflicts with remaining publishDir directives (if any)

Related

Closes #41

Review Checklist

• All publishDir directives removed from modules
• Output paths are correctly structured
• Pipeline runs successfully end-to-end
• All expected outputs appear in correct directories
• No duplicate or missing outputs

[ppreshant]

Need to change params.analysis_type to taxonomic-profiling

[ppreshant]

read again why I chose the other syntax vs this one?

mapping {
        path { "mapping/" }
    }