Multi-sample phasing for ww-glimpse2 and ww-imputation

[tefirman]

Type of Change

• Bug fix
• Documentation update

Description

Refactors glimpse2_phase_cram and the ww-imputation pipeline to support joint multi-sample phasing, aligning with the Palantir/Broad GLIMPSE2 workflow pattern.

ww-glimpse2 module

• glimpse2_phase_cram now accepts Array[File] input_bams and Array[File] input_bam_indices instead of a single file. The command block builds a bam_list.txt from the array and passes it to GLIMPSE2_phase via --bam-list, supporting both single-sample and multi-sample use cases.

ww-imputation pipeline

• Removed the ImputationSample struct and the outer per-sample scatter. All CRAMs are now passed into each glimpse2_phase_cram call for joint phasing across samples.
• The pipeline now produces a single multi-sample output file instead of one file per sample.
• Concordance is now a single optional call on the final multi-sample VCF, controlled by workflow-level truth_vcf/truth_vcf_index inputs (instead of per-sample truth VCFs in the struct).
• Added output_prefix, concat_cpu_cores, and concat_memory_gb parameters.

Related Issue

• Fixes Multi-sample phasing in glimpse2_phase_cram #240

Testing

How did you test these changes?

What workflow engine did you use?

Did the tests pass?

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)

Additional Context

This is a breaking change to the ww-imputation pipeline interface — the ImputationSample struct is removed and replaced with flat Array[File] inputs. The ww-glimpse2 module task glimpse2_phase_cram also has a breaking input signature change (File → Array[File]). Both modules are at prototype status so this is expected.