feat(chaintools): add coverage module (nextflow + wdl)

[alejandrogzi]

Wraps chaintools coverage CLI:

chaintools coverage -h

Measure annotation feature coverage by aligned chain blocks

Usage: chaintools coverage [OPTIONS] --side <SIDE> --intervals <PATH> --feature <FEATURE>

Options:
  -c, --chains <PATH>...   Input chain files. If not provided, chain data is read from standard input.
  -f, --file <PATH>        Path to a file listing one input chain path per line
      --side <SIDE>        Chain side to measure in forward genomic coordinates [possible values: reference, query]
      --intervals <PATH>   BED, GTF, or GFF annotation whose feature bases define the denominator
      --feature <FEATURE>  Annotation feature to measure [possible values: cds, exon, intron, utr]

Nextflow modules/nextflow/chaintools/coverage/main.nf:

• process CHAINTOOLS_COVERAGE (tag $meta.id, label process_low, container ghcr.io/alejandrogzi/chaintools:latest)
• inputs: tuple val(meta), path(chains) (single or List), path intervals, val side, val feature
• cmd: chaintools coverage --chains $chains --side $side --intervals $intervals --feature $feature --threads ${task.cpus} > ${prefix}.coverage.txt
• outputs: tuple val(meta), path("*.coverage.txt"), versions.yml
• follows stats/compare pattern (--threads, redirection, stub)

WDL modules/wdl/chaintools/coverage/main.wdl:

• task coverage with Array[File] chains, File intervals, String side, String feature, Int threads, extra_args, prefix
• cmd: chaintools coverage --chains ~{sep=" " chains} --side ~{side} --intervals ~{intervals} --feature ~{feature} --threads ~{threads} > ~{out_report}
• workflow run wrapper

No new dependency. Reuses existing container.

Fix from #31 already in master, this branch builds on top.