From f75106ea2925ecd93e44bcef4c696c4d41cc1a4d Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Wed, 4 Mar 2026 15:45:08 -0500
Subject: [PATCH 1/8] feat: add hlahd module (v1.7.1)

Module runs HLA-HD for HLA typing from paired-end FASTQ input.
Container-only (not available on conda/bioconda).
Private container built from JFrog-hosted binary.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 modules/msk/hlahd/environment.yml |  7 ++++
 modules/msk/hlahd/main.nf         | 66 ++++++++++++++++++++++++++++++
 modules/msk/hlahd/meta.yml        | 67 +++++++++++++++++++++++++++++++
 3 files changed, 140 insertions(+)
 create mode 100644 modules/msk/hlahd/environment.yml
 create mode 100644 modules/msk/hlahd/main.nf
 create mode 100644 modules/msk/hlahd/meta.yml

diff --git a/modules/msk/hlahd/environment.yml b/modules/msk/hlahd/environment.yml
new file mode 100644
index 00000000..4c59b932
--- /dev/null
+++ b/modules/msk/hlahd/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "YOUR-TOOL=HERE"
diff --git a/modules/msk/hlahd/main.nf b/modules/msk/hlahd/main.nf
new file mode 100644
index 00000000..dcec1e97
--- /dev/null
+++ b/modules/msk/hlahd/main.nf
@@ -0,0 +1,66 @@
+process HLAHD {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'docker://ghcr.io/mskcc-omics-workflows/hlahd:1.7.1':
+        'ghcr.io/mskcc-omics-workflows/hlahd:1.7.1' }"
+
+    input:
+    tuple val(meta), path(fastq_1), path(fastq_2)
+
+    output:
+    tuple val(meta), path("${prefix}/${prefix}_final.result.txt"), emit: result
+    tuple val(meta), path("${prefix}/result/*_result.txt"),        emit: result_per_locus
+    path "versions.yml",                                           emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args        = task.ext.args  ?: ''
+    def min_read    = task.ext.args2 ?: '100'
+    prefix          = task.ext.prefix ?: "${meta.id}"
+    def install_dir = '/opt/hlahd/current'
+    """
+    if [[ \$(ulimit -n) -lt 1024 ]]; then ulimit -n 1024; fi
+
+    ln -sf /usr/bin/python3 ./python
+    export PATH=\$PWD:\$PATH
+
+    mkdir -p ${prefix}
+
+    bash ${install_dir}/bin/hlahd.sh \\
+        -t ${task.cpus} \\
+        -m ${min_read} \\
+        -f ${install_dir}/freq_data \\
+        ${args} \\
+        ${fastq_1} \\
+        ${fastq_2} \\
+        ${install_dir}/HLA_gene.split.txt \\
+        ${install_dir}/dictionary \\
+        ${prefix} \\
+        .
+
+    HLAHD_VERSION=\$(bash ${install_dir}/bin/hlahd.sh 2>&1 | grep -oP 'HLA-HD version \\K[0-9.]+' | head -1)
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hlahd: \${HLAHD_VERSION}
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}/result
+    touch ${prefix}/${prefix}_final.result.txt
+    touch ${prefix}/result/${prefix}_A_result.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hlahd: 1.7.1
+    END_VERSIONS
+    """
+}
diff --git a/modules/msk/hlahd/meta.yml b/modules/msk/hlahd/meta.yml
new file mode 100644
index 00000000..160df59c
--- /dev/null
+++ b/modules/msk/hlahd/meta.yml
@@ -0,0 +1,67 @@
+name: "hlahd"
+description: HLA typing from paired-end FASTQ reads using HLA-HD
+keywords:
+  - HLA
+  - immunology
+  - typing
+  - genomics
+tools:
+  - "hlahd":
+      description:
+        "HLA-HD (HLA typing from High-quality Dictionary) performs HLA typing
+        from paired-end FASTQ reads using bowtie2 alignment against HLA allele dictionaries."
+      homepage: "https://w3.genome.med.kyoto-u.ac.jp/HLA-HD/"
+      documentation: "https://w3.genome.med.kyoto-u.ac.jp/HLA-HD/"
+      licence:
+        - "ACADEMIC SOFTWARE LICENSE"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fastq_1:
+        type: file
+        description: First read of paired-end FASTQ input
+        pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1930
+    - fastq_2:
+        type: file
+        description: Second read of paired-end FASTQ input
+        pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1930
+output:
+  result:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/${prefix}_final.result.txt:
+          type: file
+          description: Final HLA typing result file containing best-call alleles for all loci
+          pattern: "*_final.result.txt"
+  result_per_locus:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/result/*_result.txt:
+          type: file
+          description: Per-locus HLA typing result files (one file per HLA gene)
+          pattern: "result/*_result.txt"
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+authors:
+  - "@orgeraj"
+maintainers:
+  - "@orgeraj"

From 15ba70f55a04a29899d362b3151745d991b70e60 Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Thu, 5 Mar 2026 12:04:11 -0500
Subject: [PATCH 2/8] test: add hlahd module tests

Stub test and real test using HLA-region FASTQ from test-datasets hlahd branch.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 modules/msk/hlahd/tests/main.nf.test | 64 ++++++++++++++++++++++++++++
 modules/msk/hlahd/tests/tags.yml     |  2 +
 tests/config/test_data.config        |  6 +++
 3 files changed, 72 insertions(+)
 create mode 100644 modules/msk/hlahd/tests/main.nf.test
 create mode 100644 modules/msk/hlahd/tests/tags.yml

diff --git a/modules/msk/hlahd/tests/main.nf.test b/modules/msk/hlahd/tests/main.nf.test
new file mode 100644
index 00000000..836ec40c
--- /dev/null
+++ b/modules/msk/hlahd/tests/main.nf.test
@@ -0,0 +1,64 @@
+nextflow_process {
+
+    name "Test Process HLAHD"
+    script "../main.nf"
+    process "HLAHD"
+
+    tag "modules"
+    tag "modules_msk"
+    tag "hlahd"
+
+    test("hlahd - fastq pair - result txt") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_sample', single_end:false ], // meta map
+                    file(params.test_data_mskcc['hlahd']['fastq_1'], checkIfExists: true),
+                    file(params.test_data_mskcc['hlahd']['fastq_2'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.result,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("hlahd - fastq pair - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_sample', single_end:false ], // meta map
+                    file(params.test_data_mskcc['hlahd']['fastq_1'], checkIfExists: true),
+                    file(params.test_data_mskcc['hlahd']['fastq_2'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.result.get(0).get(1)).exists() },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/msk/hlahd/tests/tags.yml b/modules/msk/hlahd/tests/tags.yml
new file mode 100644
index 00000000..51631aae
--- /dev/null
+++ b/modules/msk/hlahd/tests/tags.yml
@@ -0,0 +1,2 @@
+hlahd:
+  - modules/msk/hlahd/**
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 30d350a6..4de5407d 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -787,6 +787,12 @@ params {
                 iedb_alignments                                = "${params.test_data_base_msk}/neoantigen/neoantigen/neoantigenEditing/data/IEDB_alignments/iedb_alignments_3-OLTS.txt"
                 test_annotated                                 = "${params.test_data_base_msk}/neoantigen/neoantigen/test_patient_test_annotated.json"
             }
+            'hlahd' {
+                fastq_1                                        = "${params.test_data_base_msk}/hlahd/hlahd/test_R1.fastq.gz"
+                fastq_2                                        = "${params.test_data_base_msk}/hlahd/hlahd/test_R2.fastq.gz"
+                bam                                            = "${params.test_data_base_msk}/hlahd/hlahd/test_hla_region.bam"
+                bai                                            = "${params.test_data_base_msk}/hlahd/hlahd/test_hla_region.bam.bai"
+            }
             'genome_nexus' {
                 test_maf                                       = "${params.test_data_base_msk}/feature/genome_nexus_subworkflow/mafs/test.maf"
                 sample2_sample1_annotated_maf                  = "${params.test_data_base_msk}/feature/genome_nexus_subworkflow/mafs/sample2_sample1_annotated.maf"

From 98749d742c33fd196a861593fc3d138ae18cfd2c Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Thu, 5 Mar 2026 12:31:12 -0500
Subject: [PATCH 3/8] feat: add hlahd_from_bam subworkflow and tests

Composes samtools/view, gatk4/revertsam (optional), samtools/fastq,
and hlahd modules into a BAM-to-HLA-typing pipeline.
Tests cover both skip_revert_sam paths plus stub test.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 subworkflows/msk/hlahd_from_bam/main.nf       |  77 +++++++++++++
 subworkflows/msk/hlahd_from_bam/meta.yml      |  68 ++++++++++++
 .../msk/hlahd_from_bam/tests/main.nf.test     | 101 ++++++++++++++++++
 .../msk/hlahd_from_bam/tests/tags.yml         |   3 +
 4 files changed, 249 insertions(+)
 create mode 100644 subworkflows/msk/hlahd_from_bam/main.nf
 create mode 100644 subworkflows/msk/hlahd_from_bam/meta.yml
 create mode 100644 subworkflows/msk/hlahd_from_bam/tests/main.nf.test
 create mode 100644 subworkflows/msk/hlahd_from_bam/tests/tags.yml

diff --git a/subworkflows/msk/hlahd_from_bam/main.nf b/subworkflows/msk/hlahd_from_bam/main.nf
new file mode 100644
index 00000000..ed8be364
--- /dev/null
+++ b/subworkflows/msk/hlahd_from_bam/main.nf
@@ -0,0 +1,77 @@
+include { SAMTOOLS_VIEW  } from '../../../modules/nf-core/samtools/view/main'
+include { GATK4_REVERTSAM } from '../../../modules/nf-core/gatk4/revertsam/main'
+include { SAMTOOLS_FASTQ } from '../../../modules/nf-core/samtools/fastq/main'
+include { HLAHD          } from '../../../modules/msk/hlahd/main'
+
+workflow HLAHD_FROM_BAM {
+
+    take:
+    ch_bam           // channel: [ val(meta), path(bam), path(bai) ]
+    skip_revert_sam  // val: Boolean
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    //
+    // MODULE: Extract HLA region from BAM using samtools view.
+    // The caller configures the region to extract via ext.args in modules.config,
+    // e.g. ext.args = '-b chr6:28000000-34000000'
+    //
+    SAMTOOLS_VIEW(
+        ch_bam,
+        [[],[]],
+        [],
+        []
+    )
+    ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first())
+
+    //
+    // Optional: Revert base quality score recalibration with GATK4 RevertSam.
+    // Set skip_revert_sam = true when the BAM has no BQSR applied (e.g. already
+    // in OQ-restored state, or produced by a tool that does not perform BQSR).
+    //
+    if (!skip_revert_sam) {
+
+        GATK4_REVERTSAM(
+            SAMTOOLS_VIEW.out.bam
+        )
+        ch_versions = ch_versions.mix(GATK4_REVERTSAM.out.versions.first())
+        ch_for_fastq = GATK4_REVERTSAM.out.bam
+
+    } else {
+
+        ch_for_fastq = SAMTOOLS_VIEW.out.bam
+
+    }
+
+    //
+    // MODULE: Convert BAM to paired FASTQ files.
+    // SAMTOOLS_FASTQ emits .out.fastq as [ meta, [fq1, fq2] ]; unpack into
+    // separate paths so HLAHD receives the three-element tuple it expects.
+    //
+    SAMTOOLS_FASTQ(
+        ch_for_fastq,
+        false
+    )
+    ch_versions = ch_versions.mix(SAMTOOLS_FASTQ.out.versions.first())
+
+    ch_fastq_for_hlahd = SAMTOOLS_FASTQ.out.fastq
+        .map { meta, fastqs ->
+            def (fq1, fq2) = fastqs
+            [meta, fq1, fq2]
+        }
+
+    //
+    // MODULE: Run HLA-HD to call HLA alleles from paired FASTQ files.
+    //
+    HLAHD(
+        ch_fastq_for_hlahd
+    )
+    ch_versions = ch_versions.mix(HLAHD.out.versions.first())
+
+    emit:
+    result           = HLAHD.out.result           // channel: [ val(meta), path(*_final.result.txt) ]
+    result_per_locus = HLAHD.out.result_per_locus // channel: [ val(meta), path(*/result/*_result.txt) ]
+    versions         = ch_versions                // channel: [ path(versions.yml) ]
+}
diff --git a/subworkflows/msk/hlahd_from_bam/meta.yml b/subworkflows/msk/hlahd_from_bam/meta.yml
new file mode 100644
index 00000000..2d209f54
--- /dev/null
+++ b/subworkflows/msk/hlahd_from_bam/meta.yml
@@ -0,0 +1,68 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "hlahd_from_bam"
+description: |
+  Extract the HLA region from a coordinate-sorted BAM file, optionally revert
+  base quality score recalibration with GATK4 RevertSam, convert to paired
+  FASTQ files with samtools fastq, and run HLA-HD for high-resolution HLA
+  typing.
+keywords:
+  - HLA
+  - typing
+  - BAM
+  - immunology
+  - samtools
+  - gatk4
+components:
+  - samtools/view
+  - gatk4/revertsam
+  - samtools/fastq
+  - hlahd
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. [ id:'sample_01', single_end:false ]
+    - bam:
+        type: file
+        description: |
+          Input BAM file. Must be coordinate-sorted and indexed.
+        pattern: "*.bam"
+    - bai:
+        type: file
+        description: BAM index file.
+        pattern: "*.bai"
+  - skip_revert_sam:
+      type: boolean
+      description: |
+        When true, skip the GATK4 RevertSam step. Set to true if the BAM was
+        not processed with base quality score recalibration (BQSR), or if
+        original base qualities have already been restored.
+output:
+  - result:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information.
+      - "*/*_final.result.txt":
+          type: file
+          description: |
+            Tab-separated HLA allele calls for all typed loci produced by
+            HLA-HD. One file per sample.
+          pattern: "*/*_final.result.txt"
+  - result_per_locus:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information.
+      - "*/result/*_result.txt":
+          type: file
+          description: Per-locus HLA result files produced by HLA-HD.
+          pattern: "*/result/*_result.txt"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions for all tools used.
+          pattern: "versions.yml"
+authors:
+  - "@orgeraj"
+maintainers:
+  - "@orgeraj"
diff --git a/subworkflows/msk/hlahd_from_bam/tests/main.nf.test b/subworkflows/msk/hlahd_from_bam/tests/main.nf.test
new file mode 100644
index 00000000..32dfdd0e
--- /dev/null
+++ b/subworkflows/msk/hlahd_from_bam/tests/main.nf.test
@@ -0,0 +1,101 @@
+nextflow_workflow {
+
+    name "Test Subworkflow HLAHD_FROM_BAM"
+    script "../main.nf"
+    workflow "HLAHD_FROM_BAM"
+
+    tag "subworkflows"
+    tag "subworkflows_msk"
+    tag "subworkflows/hlahd_from_bam"
+    tag "hlahd_from_bam"
+    tag "hlahd"
+    tag "samtools"
+    tag "gatk4"
+
+    test("hlahd_from_bam - bam - with revert sam - result") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [ id:'test_sample', single_end:false ], // meta map
+                    file(params.test_data_mskcc['hlahd']['bam'], checkIfExists: true),
+                    file(params.test_data_mskcc['hlahd']['bai'], checkIfExists: true)
+                    ])
+
+                input[1] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.result,
+                    workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("hlahd_from_bam - bam - skip revert sam - result") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [ id:'test_sample', single_end:false ], // meta map
+                    file(params.test_data_mskcc['hlahd']['bam'], checkIfExists: true),
+                    file(params.test_data_mskcc['hlahd']['bai'], checkIfExists: true)
+                    ])
+
+                input[1] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.result,
+                    workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("hlahd_from_bam - bam - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.value([
+                    [ id:'test_sample', single_end:false ], // meta map
+                    file('test_hla_region.bam', checkIfExists: false),
+                    file('test_hla_region.bam.bai', checkIfExists: false)
+                    ])
+
+                input[1] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.result[0][0],
+                    file(workflow.out.result[0][1]).name,
+                    workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+}
diff --git a/subworkflows/msk/hlahd_from_bam/tests/tags.yml b/subworkflows/msk/hlahd_from_bam/tests/tags.yml
new file mode 100644
index 00000000..4da44ddc
--- /dev/null
+++ b/subworkflows/msk/hlahd_from_bam/tests/tags.yml
@@ -0,0 +1,3 @@
+subworkflows/hlahd_from_bam:
+  - subworkflows/msk/hlahd_from_bam/**
+  - modules/msk/hlahd/**

From 459877e7bfe854138566ccc1d05768f608768dc7 Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Thu, 5 Mar 2026 17:42:19 -0500
Subject: [PATCH 4/8] fix: update hlahd container URL to JFrog registry

Also add the nf-test snapshot file that was missing from prior commits.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 modules/msk/hlahd/main.nf                 |  4 ++--
 modules/msk/hlahd/tests/main.nf.test.snap | 29 +++++++++++++++++++++++
 2 files changed, 31 insertions(+), 2 deletions(-)
 create mode 100644 modules/msk/hlahd/tests/main.nf.test.snap

diff --git a/modules/msk/hlahd/main.nf b/modules/msk/hlahd/main.nf
index dcec1e97..c768bfad 100644
--- a/modules/msk/hlahd/main.nf
+++ b/modules/msk/hlahd/main.nf
@@ -4,8 +4,8 @@ process HLAHD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://ghcr.io/mskcc-omics-workflows/hlahd:1.7.1':
-        'ghcr.io/mskcc-omics-workflows/hlahd:1.7.1' }"
+        'docker://mskcc.jfrog.io/omicswf-docker-prod-local/mskcc-omics-workflows/hlahd:1.7.1':
+        'mskcc.jfrog.io/omicswf-docker-prod-local/mskcc-omics-workflows/hlahd:1.7.1' }"
 
     input:
     tuple val(meta), path(fastq_1), path(fastq_2)
diff --git a/modules/msk/hlahd/tests/main.nf.test.snap b/modules/msk/hlahd/tests/main.nf.test.snap
new file mode 100644
index 00000000..795b0ca6
--- /dev/null
+++ b/modules/msk/hlahd/tests/main.nf.test.snap
@@ -0,0 +1,29 @@
+{
+    "hlahd - fastq pair - stub": {
+        "content": [
+            [
+                "versions.yml:md5,f196d451477cda61837f7cfb2ed3c9b4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-03-05T16:10:44.004384"
+    },
+    "hlahd - fastq pair - result txt": {
+        "content": [
+            [
+                
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-03-05T16:10:39.867251"
+    }
+}
\ No newline at end of file

From 2278abf0ef6b395dc8aaa68f8bfbe5c4bffa0f56 Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Mon, 9 Mar 2026 13:36:07 -0400
Subject: [PATCH 5/8] fix: correct HLAHD output paths, update container to dev,
 refresh snapshots

- Fix output globs: results are at <prefix>/result/, not <prefix>/
  - result: ${prefix}/result/${prefix}_final.result.txt
  - result_per_locus: ${prefix}/result/${prefix}_*.est.txt
- Switch container URL to dev registry while awaiting next prod release
- Add nextflow.config for subworkflow tests (ext.prefix per process to
  avoid GATK4_REVERTSAM input/output name collision)
- Regenerate all snapshots against new HLA class I test data that
  produces actual allele calls (A*01:01:01, B*08:01:01, C*07:01:01)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 modules/msk/hlahd/main.nf                     | 18 +++--
 modules/msk/hlahd/meta.yml                    | 10 +--
 modules/msk/hlahd/tests/main.nf.test.snap     | 20 ++++--
 subworkflows/msk/hlahd_from_bam/main.nf       |  4 +-
 subworkflows/msk/hlahd_from_bam/meta.yml      | 10 +--
 .../msk/hlahd_from_bam/tests/main.nf.test     |  5 ++
 .../hlahd_from_bam/tests/main.nf.test.snap    | 69 +++++++++++++++++++
 .../msk/hlahd_from_bam/tests/nextflow.config  | 11 +++
 8 files changed, 118 insertions(+), 29 deletions(-)
 create mode 100644 subworkflows/msk/hlahd_from_bam/tests/main.nf.test.snap
 create mode 100644 subworkflows/msk/hlahd_from_bam/tests/nextflow.config

diff --git a/modules/msk/hlahd/main.nf b/modules/msk/hlahd/main.nf
index c768bfad..56039658 100644
--- a/modules/msk/hlahd/main.nf
+++ b/modules/msk/hlahd/main.nf
@@ -4,15 +4,15 @@ process HLAHD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://mskcc.jfrog.io/omicswf-docker-prod-local/mskcc-omics-workflows/hlahd:1.7.1':
-        'mskcc.jfrog.io/omicswf-docker-prod-local/mskcc-omics-workflows/hlahd:1.7.1' }"
+        'docker://mskcc.jfrog.io/omicswf-docker-dev-local/mskcc-omics-workflows/hlahd:1.7.1':
+        'mskcc.jfrog.io/omicswf-docker-dev-local/mskcc-omics-workflows/hlahd:1.7.1' }"
 
     input:
     tuple val(meta), path(fastq_1), path(fastq_2)
 
     output:
-    tuple val(meta), path("${prefix}/${prefix}_final.result.txt"), emit: result
-    tuple val(meta), path("${prefix}/result/*_result.txt"),        emit: result_per_locus
+    tuple val(meta), path("${prefix}/result/${prefix}_final.result.txt"), emit: result
+    tuple val(meta), path("${prefix}/result/${prefix}_*.est.txt"),       emit: result_per_locus
     path "versions.yml",                                           emit: versions
 
     when:
@@ -43,11 +43,9 @@ process HLAHD {
         ${prefix} \\
         .
 
-    HLAHD_VERSION=\$(bash ${install_dir}/bin/hlahd.sh 2>&1 | grep -oP 'HLA-HD version \\K[0-9.]+' | head -1)
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        hlahd: \${HLAHD_VERSION}
+        hlahd: \$(bash ${install_dir}/bin/hlahd.sh 2>&1 | grep -oP 'HLA-HD version \\K[0-9.]+' | head -1)
     END_VERSIONS
     """
 
@@ -55,12 +53,12 @@ process HLAHD {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p ${prefix}/result
-    touch ${prefix}/${prefix}_final.result.txt
-    touch ${prefix}/result/${prefix}_A_result.txt
+    touch ${prefix}/result/${prefix}_final.result.txt
+    touch ${prefix}/result/${prefix}_A.est.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        hlahd: 1.7.1
+        hlahd: \$(bash /opt/hlahd/current/bin/hlahd.sh 2>&1 | grep -oP 'HLA-HD version \\K[0-9.]+' | head -1)
     END_VERSIONS
     """
 }
diff --git a/modules/msk/hlahd/meta.yml b/modules/msk/hlahd/meta.yml
index 160df59c..3d1c6442 100644
--- a/modules/msk/hlahd/meta.yml
+++ b/modules/msk/hlahd/meta.yml
@@ -40,20 +40,20 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - ${prefix}/${prefix}_final.result.txt:
+      - ${prefix}/result/${prefix}_final.result.txt:
           type: file
           description: Final HLA typing result file containing best-call alleles for all loci
-          pattern: "*_final.result.txt"
+          pattern: "**/result/*_final.result.txt"
   result_per_locus:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - ${prefix}/result/*_result.txt:
+      - ${prefix}/result/${prefix}_*.est.txt:
           type: file
-          description: Per-locus HLA typing result files (one file per HLA gene)
-          pattern: "result/*_result.txt"
+          description: Per-locus HLA estimation files (one file per HLA gene)
+          pattern: "**/result/*_*.est.txt"
   versions:
     - versions.yml:
         type: file
diff --git a/modules/msk/hlahd/tests/main.nf.test.snap b/modules/msk/hlahd/tests/main.nf.test.snap
index 795b0ca6..0184980d 100644
--- a/modules/msk/hlahd/tests/main.nf.test.snap
+++ b/modules/msk/hlahd/tests/main.nf.test.snap
@@ -5,25 +5,31 @@
                 "versions.yml:md5,f196d451477cda61837f7cfb2ed3c9b4"
             ]
         ],
+        "timestamp": "2026-03-05T16:10:44.004384",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-05T16:10:44.004384"
+        }
     },
     "hlahd - fastq pair - result txt": {
         "content": [
             [
-                
+                [
+                    {
+                        "id": "test_sample",
+                        "single_end": false
+                    },
+                    "test_sample_final.result.txt:md5,6f83fc8ac5bd3b9f56853b583595e2a0"
+                ]
             ],
             [
-                
+                "versions.yml:md5,f196d451477cda61837f7cfb2ed3c9b4"
             ]
         ],
+        "timestamp": "2026-03-09T11:03:42.014639",
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-05T16:10:39.867251"
+        }
     }
 }
\ No newline at end of file
diff --git a/subworkflows/msk/hlahd_from_bam/main.nf b/subworkflows/msk/hlahd_from_bam/main.nf
index ed8be364..4ca7a195 100644
--- a/subworkflows/msk/hlahd_from_bam/main.nf
+++ b/subworkflows/msk/hlahd_from_bam/main.nf
@@ -71,7 +71,7 @@ workflow HLAHD_FROM_BAM {
     ch_versions = ch_versions.mix(HLAHD.out.versions.first())
 
     emit:
-    result           = HLAHD.out.result           // channel: [ val(meta), path(*_final.result.txt) ]
-    result_per_locus = HLAHD.out.result_per_locus // channel: [ val(meta), path(*/result/*_result.txt) ]
+    result           = HLAHD.out.result           // channel: [ val(meta), path(result/*_final.result.txt) ]
+    result_per_locus = HLAHD.out.result_per_locus // channel: [ val(meta), path(result/*_*.est.txt) ]
     versions         = ch_versions                // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/msk/hlahd_from_bam/meta.yml b/subworkflows/msk/hlahd_from_bam/meta.yml
index 2d209f54..4bdbb82f 100644
--- a/subworkflows/msk/hlahd_from_bam/meta.yml
+++ b/subworkflows/msk/hlahd_from_bam/meta.yml
@@ -43,20 +43,20 @@ output:
       - meta:
           type: map
           description: Groovy Map containing sample information.
-      - "*/*_final.result.txt":
+      - "**/result/*_final.result.txt":
           type: file
           description: |
             Tab-separated HLA allele calls for all typed loci produced by
             HLA-HD. One file per sample.
-          pattern: "*/*_final.result.txt"
+          pattern: "**/result/*_final.result.txt"
   - result_per_locus:
       - meta:
           type: map
           description: Groovy Map containing sample information.
-      - "*/result/*_result.txt":
+      - "**/result/*_*.est.txt":
           type: file
-          description: Per-locus HLA result files produced by HLA-HD.
-          pattern: "*/result/*_result.txt"
+          description: Per-locus HLA estimation files produced by HLA-HD.
+          pattern: "**/result/*_*.est.txt"
   - versions:
       - "versions.yml":
           type: file
diff --git a/subworkflows/msk/hlahd_from_bam/tests/main.nf.test b/subworkflows/msk/hlahd_from_bam/tests/main.nf.test
index 32dfdd0e..3e817f9a 100644
--- a/subworkflows/msk/hlahd_from_bam/tests/main.nf.test
+++ b/subworkflows/msk/hlahd_from_bam/tests/main.nf.test
@@ -14,6 +14,8 @@ nextflow_workflow {
 
     test("hlahd_from_bam - bam - with revert sam - result") {
 
+        config "./nextflow.config"
+
         when {
             workflow {
                 """
@@ -42,6 +44,8 @@ nextflow_workflow {
 
     test("hlahd_from_bam - bam - skip revert sam - result") {
 
+        config "./nextflow.config"
+
         when {
             workflow {
                 """
@@ -70,6 +74,7 @@ nextflow_workflow {
 
     test("hlahd_from_bam - bam - stub") {
 
+        config "./nextflow.config"
         options "-stub"
 
         when {
diff --git a/subworkflows/msk/hlahd_from_bam/tests/main.nf.test.snap b/subworkflows/msk/hlahd_from_bam/tests/main.nf.test.snap
new file mode 100644
index 00000000..ac039f62
--- /dev/null
+++ b/subworkflows/msk/hlahd_from_bam/tests/main.nf.test.snap
@@ -0,0 +1,69 @@
+{
+    "hlahd_from_bam - bam - stub": {
+        "content": [
+            {
+                "id": "test_sample",
+                "single_end": false
+            },
+            "test_sample_final.result.txt",
+            [
+                "versions.yml:md5,181590c9fdbd5c2815c3ce5208703884",
+                "versions.yml:md5,3536f6f188f43e5bb192831b7809a671",
+                "versions.yml:md5,475acfad0fe45163f0020ba941a658c1",
+                "versions.yml:md5,e0264ab44efbd0fd97853a90160075a1"
+            ]
+        ],
+        "timestamp": "2026-03-09T12:50:14.479909",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "hlahd_from_bam - bam - skip revert sam - result": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_sample",
+                        "single_end": false
+                    },
+                    "test_sample_final.result.txt:md5,6f83fc8ac5bd3b9f56853b583595e2a0"
+                ]
+            ],
+            [
+                "versions.yml:md5,181590c9fdbd5c2815c3ce5208703884",
+                "versions.yml:md5,475acfad0fe45163f0020ba941a658c1",
+                "versions.yml:md5,e0264ab44efbd0fd97853a90160075a1"
+            ]
+        ],
+        "timestamp": "2026-03-09T12:49:52.217786",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "hlahd_from_bam - bam - with revert sam - result": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_sample",
+                        "single_end": false
+                    },
+                    "test_sample_final.result.txt:md5,6f83fc8ac5bd3b9f56853b583595e2a0"
+                ]
+            ],
+            [
+                "versions.yml:md5,181590c9fdbd5c2815c3ce5208703884",
+                "versions.yml:md5,3536f6f188f43e5bb192831b7809a671",
+                "versions.yml:md5,475acfad0fe45163f0020ba941a658c1",
+                "versions.yml:md5,e0264ab44efbd0fd97853a90160075a1"
+            ]
+        ],
+        "timestamp": "2026-03-09T12:33:58.060705",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/msk/hlahd_from_bam/tests/nextflow.config b/subworkflows/msk/hlahd_from_bam/tests/nextflow.config
new file mode 100644
index 00000000..cca601fd
--- /dev/null
+++ b/subworkflows/msk/hlahd_from_bam/tests/nextflow.config
@@ -0,0 +1,11 @@
+process {
+    withName: 'HLAHD_FROM_BAM:SAMTOOLS_VIEW' {
+        ext.prefix = { "${meta.id}.hla_region" }
+    }
+    withName: 'HLAHD_FROM_BAM:GATK4_REVERTSAM' {
+        ext.prefix = { "${meta.id}.reverted" }
+    }
+    withName: 'HLAHD_FROM_BAM:SAMTOOLS_FASTQ' {
+        ext.prefix = { "${meta.id}" }
+    }
+}

From 13a2ba3cb98731f920d07d6a8e3d96c87171c97a Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Mon, 9 Mar 2026 18:38:52 -0400
Subject: [PATCH 6/8] fix: update author/maintainer to GitHub username

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 modules/msk/hlahd/meta.yml               | 4 ++--
 subworkflows/msk/hlahd_from_bam/meta.yml | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/msk/hlahd/meta.yml b/modules/msk/hlahd/meta.yml
index 3d1c6442..b268a910 100644
--- a/modules/msk/hlahd/meta.yml
+++ b/modules/msk/hlahd/meta.yml
@@ -62,6 +62,6 @@ output:
         ontologies:
           - edam: http://edamontology.org/format_3750
 authors:
-  - "@orgeraj"
+  - "@johnoooh"
 maintainers:
-  - "@orgeraj"
+  - "@johnoooh"
diff --git a/subworkflows/msk/hlahd_from_bam/meta.yml b/subworkflows/msk/hlahd_from_bam/meta.yml
index 4bdbb82f..8dfd5366 100644
--- a/subworkflows/msk/hlahd_from_bam/meta.yml
+++ b/subworkflows/msk/hlahd_from_bam/meta.yml
@@ -63,6 +63,6 @@ output:
           description: File containing software versions for all tools used.
           pattern: "versions.yml"
 authors:
-  - "@orgeraj"
+  - "@johnoooh"
 maintainers:
-  - "@orgeraj"
+  - "@johnoooh"

From e4601248d94edc00fbf1bc48376377666a8f4c40 Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Fri, 20 Mar 2026 11:24:57 -0400
Subject: [PATCH 7/8] ci: add JFrog registry authentication to nf-test workflow

Add docker/login-action step to authenticate with mskcc.jfrog.io before
running tests. Login is conditional on docker profile and credentials being
present, so conda/singularity profiles are unaffected.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .github/actions/nf-test-action/action.yml | 16 ++++++++++++++++
 .github/workflows/nf-test.yml             |  2 ++
 2 files changed, 18 insertions(+)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 799e5db0..61ccbc2d 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -13,6 +13,14 @@ inputs:
   paths:
     description: "Test paths"
     required: true
+  jfrog_username:
+    description: "JFrog registry username"
+    required: false
+    default: ""
+  jfrog_password:
+    description: "JFrog registry password or token"
+    required: false
+    default: ""
 
 runs:
   using: "composite"
@@ -72,6 +80,14 @@ runs:
         nextflow secrets set ONCOKB_TOKEN $ONCOKB_TOKEN
 
 
+    - name: Login to JFrog Container Registry
+      if: ${{ inputs.profile == 'docker' && inputs.jfrog_username != '' }}
+      uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567 # v3
+      with:
+        registry: mskcc.jfrog.io
+        username: ${{ inputs.jfrog_username }}
+        password: ${{ inputs.jfrog_password }}
+
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 30223b81..e41e3532 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -135,6 +135,8 @@ jobs:
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
           paths: "${{ join(fromJson(steps.filter.outputs.filtered_paths), ' ') }}"
+          jfrog_username: ${{ secrets.JFROG_USERNAME }}
+          jfrog_password: ${{ secrets.JFROG_PASSWORD }}
 
   confirm-pass:
     runs-on: ubuntu-latest

From 3d733d6f1d1fc0cd188f3b226adc1137db3f43ec Mon Sep 17 00:00:00 2001
From: John Orgera <65687576+johnoooh@users.noreply.github.com>
Date: Fri, 20 Mar 2026 11:28:03 -0400
Subject: [PATCH 8/8] ci: skip hlahd module and subworkflow for conda profile

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .github/skip_nf_test.json | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/skip_nf_test.json b/.github/skip_nf_test.json
index 58ef7e41..85634e98 100644
--- a/.github/skip_nf_test.json
+++ b/.github/skip_nf_test.json
@@ -36,7 +36,9 @@
         "subworkflows/msk/phylowgs",
         "subworkflows/msk/generate_mutated_peptides",
         "subworkflows/msk/neoantigen_editing",
-        "subworkflows/msk/traceback"
+        "subworkflows/msk/traceback",
+        "modules/msk/hlahd",
+        "subworkflows/msk/hlahd_from_bam"
     ],
     "docker": [],
     "singularity": []