feat(samtools/view): add -L option for BED file filtering

[luisas]

Add optional 'bed' input channel to SAMTOOLS_VIEW process to support filtering alignments by genomic region using the samtools -L flag.

Changes:

• main.nf: add 'path bed' input, 'def bedfile' variable, and ${bedfile} in command
• meta.yml: document new 'bed' input with EDAM ontology
• tests/main.nf.test: shift index_format from input[3] to input[4] in all existing tests (insert input[3] = [] for bed), and add new bam_with_bed test

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