Add mosdepth

[lazappi]

Description

Add a component for mosdepth, a tool for fast calculation of coverage depth.

Checklist before requesting a review

• I have performed a self-review of my code

• Conforms to the Contributing guidelines

• Proposed changes are described in the CHANGELOG.md

• I have tested my code with viash ns test --parallel -q <name or namespace>

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Documentation
  • Bug fixes

[mdgrv]

Restrict --output_regions/--output_region_dist output to windows of this fixed size (an integer). To use a BED file of regions instead, pass it to --by_bed. One of --by/--by_bed is required in order to
use --thresholds.

[mdgrv]

    example: 500
  - name: "--by_bed"
    type: file
    description: |
      BED file of regions to restrict `--output_regions`/
      `--output_region_dist` output to, as an alternative to the fixed-window
      `--by`. Mutually exclusive with `--by`. This is a separate file-typed
      argument (rather than reusing `--by`) so it is staged into the
      container.
    example: regions.bed

[mdgrv]

# mosdepth's --by accepts either a fixed window size (integer) or a BED file.
# The BED case is exposed as a separate file-typed argument (--by_bed) so it is
# staged into the container; whichever is set is passed to mosdepth's --by.
by_value="$par_by"
if [ -n "$par_by_bed" ]; then
  if [ -n "$par_by" ]; then
    echo "Error: --by and --by_bed are mutually exclusive." >&2
    exit 1
  fi
  by_value="$par_by_bed"
fi

[mdgrv]

${by_value:+--by "$by_value"}

[mdgrv]

##############################################################
log "Starting TEST 10: BED-file regions via --by_bed"
##############################################################
printf 'chr1\t100\t300\tregionA\n' >"$meta_temp_dir/regions.bed"
"$meta_executable"
--input "$bam"
--input_index "$bai"
--by_bed "$meta_temp_dir/regions.bed"
--no_per_base
--output_regions "$meta_temp_dir/test10_regions.bed.gz"
--output_regions_index "$meta_temp_dir/test10_regions.bed.gz.csi"

check_file_exists "$meta_temp_dir/test10_regions.bed.gz" "Regions output (--by_bed)"
check_file_not_empty "$meta_temp_dir/test10_regions.bed.gz" "Regions output (--by_bed)"
check_file_exists "$meta_temp_dir/test10_regions.bed.gz.csi" "Regions output index (--by_bed)"
gunzip -c "$meta_temp_dir/test10_regions.bed.gz" >"$meta_temp_dir/test10_regions.bed"
check_file_contains "$meta_temp_dir/test10_regions.bed" "regionA" "Regions output (--by_bed)"
log "✅ TEST 10 completed successfully"

[mdgrv]

The component is clean and follows the biobox conventions
throughout (script rules, pinned container + software_versions.txt, ASCII, CHANGELOG
cites the PR). viash ns test is green and the numbers are correct on real data: on an
HG002 HiFi chr21 BAM, mosdepth's summary mean depth matches samtools coverage
(23.28 vs 23.2758).

One blocking issue, found on real data:

--by with a BED file fails under the Docker runner. --by is type: string, so a
BED file passed to it is never staged into the container - viash only mounts
type: file arguments. mosdepth then errors before reading any coverage:

[E::hts_open_format] Failed to open file ".../regions.bed" : No such file or directory

The integer-window form of --by works (a number needs no file), and CRAM works
(--fasta is type: file), so only the BED-interval form is affected. It's
data-independent - it reproduces on the shipped synthetic test BAM too - and the current
tests don't catch it because TEST 2/5 only pass an integer (--by 100).

Suggested fix: expose the BED case as a separate file-typed argument (--by_bed) so
viash mounts it, and route whichever of --by/--by_bed is set to mosdepth's --by.
Committable suggestions below, plus a test that passes a real BED. I applied and
validated exactly this in a local worktree: viash ns test passes (now 10 tests), the
real-data --by_bed run returns chr21 15000000 35000000 54.31 (== samtools 54.3115),
integer --by still works, and --by + --by_bed together errors as expected.