Adding initial draft of ww-mosdepth WILDS WDL module

[tefirman]

Type of Change

• New module

Description

Adds an initial draft of the ww-mosdepth module, wrapping mosdepth (Pedersen & Quinlan, 2018) for fast per-base, per-region, and per-window coverage depth calculation from BAM/CRAM alignments. The module exposes a single calculate_depth task with optional reference FASTA (for CRAM), optional regions BED, and a configurable window size (default 100bp). Uses the pinned getwilds/mosdepth:0.3.14 container image, includes a zero-config testrun.wdl that pulls test data via ww-testdata, and ships a README documenting inputs, outputs, usage, and citation.

Testing

How did you test these changes?
Ran testrun.wdl with auto-provisioned test BAM and hg38 chr1 reference from ww-testdata, scattered over a single demo sample.

What workflow engine did you use?
Sprocket locally; CI will exercise Cromwell, miniWDL, and Sprocket.

Did the tests pass?
Yes.

Documentation

• I updated the README (if applicable)
• I added/updated parameter descriptions in the WDL (if applicable)
• I ran make docs-preview to check documentation rendering (if applicable)