mosdepth cov stat

[bshifaw]

Adding workflow that generates a set of coverage stats for a BAM file using Mosdepth.
Output results to a CSV file and JSON value
Output stat includes:

1. evenness_score_coverage
2. iqr_coverage
3. mad_coverage
4. mean_coverage
5. median_coverage
6. percent_above_4x_coverage
7. q1_coverage
8. q3_coverage
9. sstdev_coverage

[Copilot]

Pull Request Overview

This PR introduces a new WDL workflow to compute coverage statistics using mosdepth and registers it in Dockstore.

• Adds MosdepthCoverageStats workflow with options for summary and per-interval stats, including filtering and binning.
• Implements three core tasks: MosDepthOverBed, MosDepthPerInterval, and BinBed, plus a failure handler.
• Updates .dockstore.yml to include the new CoverageStats workflow.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
wdl/pipelines/TechAgnostic/Utility/CoverageStats.wdl	New workflow and tasks to generate coverage stats via mosdepth.
.dockstore.yml	Registers the CoverageStats workflow for Dockstore publishing.

Comments suppressed due to low confidence (2)

wdl/pipelines/TechAgnostic/Utility/CoverageStats.wdl:6

• [nitpick] The workflow description could be expanded to briefly outline the output artifacts (e.g., CSV and JSON summary files) and key metrics calculated for better user guidance.

description: "Calculate coverage statistics using mosdepth."

wdl/pipelines/TechAgnostic/Utility/CoverageStats.wdl:3

• There are no accompanying tests or validation workflows for the new MosdepthCoverageStats workflow. Consider adding WDL unit or integration tests to verify key branches (e.g., with and without bed files and stats_per_interval).

workflow MosdepthCoverageStats {

[Copilot]

The empty bed-file check is applied whenever bed_file is defined, even if stats_per_interval is false. Consider moving this validation inside the stats_per_interval block or adding a condition to only fail when stats_per_interval is true.

Suggested change

	if (defined(bed_file)) {
	if (length(read_lines(select_first([bed_file]))) == 0) {
	call FailWorkflow as EmptyBedFile {
	input:
	message = "stats_per_interval is set to true, but the provided bed file is empty."
	}
	}
	}
	# Empty bed file check moved into stats_per_interval block.

[Copilot]

[nitpick] The MosDepthOverBed and MosDepthPerInterval tasks share many duplicated inputs and parameters. Consider factoring common logic into a separate subtask or parameterized call to reduce duplication and simplify maintenance.