Phase 2 migration architecture

Workflow graph

GRMAP_CORE subworkflow:

• MATCH
• ANNOTATE

Downstream workflow:

• MERGE_ANNOTATED
• SUMMARIZE_MATCHES
• PLOT_COUNTS_AND_CPG_GC
• PLOT_TSS_DISTANCE
• PLOT_TSS_TYPE

Design choices

• Keep Perl scripts as computational core.
• Use metadata map (meta) through channels with sample, chromosome, and annotation file paths.
• Support two input modes:
• --input glob (legacy-compatible defaults, chr1).
• --samplesheet CSV (multi-chromosome-ready, explicit file mapping).

Repository layout

• main.nf, nextflow.config, nextflow_schema.json
• conf/ profile and default parameter composition
• modules/local/ process modules
• subworkflows/local/ orchestration
• workflows/ entry workflow
• assets/samplesheet.csv example
• tests/ smoke + perl checks
• docs/ MkDocs Material documentation