Multi-chromosome extension guide

Where chr1 was hard-coded historically

• Snakemake annotate rule used fixed chr1 filenames.
• scripts/annotate.pl assigned chr1 internally for all matches.

What changed

• annotate.pl now accepts optional chromosome argument ([chromosome], default chr1).
• Nextflow metadata map carries chromosome, gff, tss, cpg, repeatmasker per sample row.

Recommended scaling pattern

Use --samplesheet with one row per (sample, chromosome annotation set).

sample,reads,chromosome,gff,tss,cpg,repeatmasker
sampleA_chr1,reads_A.fasta.gz,chr1,chr1.gff3.gz,chr1_tss.txt.gz,cpg.txt.gz,repeatmasker.bed.gz
sampleA_chr2,reads_A.fasta.gz,chr2,chr2.gff3.gz,chr2_tss.txt.gz,cpg.txt.gz,repeatmasker.bed.gz

This pattern propagates chromosome metadata in channels and keeps output naming sample-scoped.

Future enhancement path

If match coordinates become multi-chromosome aware, pass chromosome directly from matcher output instead of fixed per-row metadata.