Add HLA-HD v1.7.1 module and BAM-input subworkflow

[johnoooh]

Add HLA-HD v1.7.1 module and BAM-input subworkflow

Summary

• Adds modules/msk/hlahd — nf-core-style module for HLA-HD v1.7.1 (high-resolution HLA typing from paired FASTQ)
• Adds subworkflows/msk/hlahd_from_bam — end-to-end BAM-to-HLA-typing workflow
• Adds test data entries to tests/config/test_data.config (data on hlahd branch of test-datasets repo)

Module: modules/msk/hlahd

Container	mskcc.jfrog.io/omicswf-docker-dev-local/mskcc-omics-workflows/hlahd:1.7.1
Input	[ meta, fastq_1, fastq_2 ]
Output	result (final allele calls), result_per_locus (per-gene .est.txt files), versions

• Min-read threshold configurable via ext.args2 (default: 100)
• Includes stub for pipeline dry-runs

Note: Container currently points to the dev registry. Will be updated to prod on the next containers release.

Subworkflow: subworkflows/msk/hlahd_from_bam

Chains four modules to go from coordinate-sorted BAM to HLA allele calls:

[ meta, bam, bai ]
        |
  SAMTOOLS_VIEW         extract HLA region (configured via ext.args)
        |
  GATK4_REVERTSAM       optional BQSR reversion (skip_revert_sam param)
        |
  SAMTOOLS_FASTQ        BAM -> paired FASTQ
        |
  HLAHD                 HLA allele calling
        |
[ result, result_per_locus, versions ]

The skip_revert_sam parameter controls whether GATK4 RevertSam runs. Set to true when the input BAM has no BQSR applied.

Add HLA-HD v1.7.1 module and BAM-input subworkflow

• Adds subworkflows/msk/hlahd_from_bam — end-to-end BAM-to-HLA-typing workflow

Module: modules/msk/hlahd

Container	mskcc.jfrog.io/omicswf-docker-dev-local/mskcc-omics-workflows/hlahd:1.7.1
Input	[ meta, fastq_1, fastq_2 ]

• Min-read threshold configurable via ext.args2 (default: 100)
• Includes stub for pipeline dry-runs

Subworkflow: subworkflows/msk/hlahd_from_bam

Chains four modules to go from coordinate-sorted BAM to HLA allele calls:

[ meta, bam, bai ]
        |
  SAMTOOLS_VIEW         extract HLA region (configured via ext.args)
        |
  GATK4_REVERTSAM       optional BQSR reversion (skip_revert_sam param)
        |
  SAMTOOLS_FASTQ        BAM -> paired FASTQ
        |
  HLAHD                 HLA allele calling
        |
[ result, result_per_locus, versions ]

Test data

Region	Coordinates (GRCh37)
HLA-A	6:29910247-29913661
HLA-B	6:31321649-31324989
HLA-C	6:31236526-31239913

~21k reads, ~3.3MB across 4 files (BAM + BAI + paired FASTQ).

Example output (test_sample_final.result.txt)

A       HLA-A*01:01:01  HLA-A*29:02:01
B       HLA-B*08:01:01  HLA-B*44:46
C       HLA-C*07:01:01  HLA-C*16:26
DRB1    Not typed       Not typed
        |
[ result, result_per_locus, versions ]

Class II loci are "Not typed" as expected — only class I regions are included in the test data.

Tests

All 5 nf-test tests pass with deterministic snapshot matching:

Module tests (2):

• hlahd - fastq pair - result txt — real HLA-HD run, verifies final result md5
• hlahd - fastq pair - stub — stub run, verifies versions output

Subworkflow tests (3):

• hlahd_from_bam - bam - with revert sam - result — full pipeline with GATK4 RevertSam
• hlahd_from_bam - bam - skip revert sam - result — pipeline skipping RevertSam
• hlahd_from_bam - bam - stub — stub run

Both revert/skip-revert paths produce identical final calls (md5: 6f83fc8ac5bd3b9f56853b583595e2a0).

Checklist

• Module follows nf-core conventions (meta map, ext.args, versions.yml)
• All 5 nf-test tests passing
• Snapshot files committed
• Test data on hlahd branch in test-datasets repo
• meta.yml complete for both module and subworkflow
• Container URL switched to prod registry (pending next containers release)