Module/oncokb maf annotation

.github/CODEOWNERS

@@ -20,6 +20,7 @@ modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
+modules/msk/oncokb/mafannotate/** @johnoooh @mskcc-omics-workflows/reviewers
 modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers
 modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers

.github/actions/nf-test-action/action.yml

@@ -65,6 +65,13 @@ runs:
         python -m pip install cryptography
         nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
 
+    - name: Set up nextflow ONCOKB secrets
+      if: env.ONCOKB_TOKEN != '' 
+      shell: bash
+      run: |
+        nextflow secrets set ONCOKB_TOKEN $ONCOKB_TOKEN
+
+
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test

.github/conda_skip.yml

@@ -74,3 +74,5 @@ exclude:
     path: modules/msk/neosv
   - profile: conda
     path: modules/msk/netmhc3
+  - profile: conda
+    path: modules/msk/oncokb/mafannotate

.github/skip_nf_test.json

@@ -28,7 +28,8 @@
         "modules/msk/phylowgs/parsecnvs",
         "modules/msk/pvmaf/concat",
         "modules/msk/pvmaf/tagtraceback",
-        "subworkflows/msk/genome_nexus"
+        "subworkflows/msk/genome_nexus",
+        "modules/msk/oncokb/mafannotate"
     ],
     "docker": [
     ],

.github/workflows/nf-test.yml

@@ -79,7 +79,6 @@ jobs:
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: 5
-
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
@@ -130,6 +129,7 @@ jobs:
           SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
           SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
           SENTIEON_AUTH_MECH: "GitHub Actions - token"
+          ONCOKB_TOKEN: ${{ secrets.ONCOKB_TOKEN }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}

modules/msk/oncokb/mafannotate/environment.yml

@@ -0,0 +1,6 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "oncokb=version"

modules/msk/oncokb/mafannotate/main.nf

@@ -0,0 +1,51 @@
+process ONCOKB_MAFANNOTATE {
+    tag "$meta.id"
+    label 'process_single'
+
+    secret 'ONCOKB_TOKEN'
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/mskcc-omics-workflows/oncokb:3.4.1':
+        'ghcr.io/mskcc-omics-workflows/oncokb:3.4.1' }"
+
+    input:
+    tuple val(meta),  path(inputMaf)
+
+    output:
+    tuple val(meta), path("*.oncokb.maf"),     emit: oncokb_maf
+    path "versions.yml",                       emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    python3 /usr/bin/oncokb/MafAnnotator.py \
+    -i ${inputMaf} \
+    -o ${prefix}.oncokb.maf \
+    -b ${ONCOKB_TOKEN}
+    $args
+
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            MafAnnotator: \$(echo \$(MafAnnotator.py -v))
+        END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+        mkdir ${prefix}_out
+        touch ${prefix}.oncokb.maf
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            MafAnnotator: \$(echo \$(MafAnnotator.py -v))
+        END_VERSIONS
+    """
+}

modules/msk/oncokb/mafannotate/meta.yml

@@ -0,0 +1,46 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "oncokb_mafannotate"
+description:
+  Takes a Maf and annotates it using OncoKB.
+keywords:
+  - oncokb
+  - maf
+  - annotation
+tools:
+  - oncokb:
+      description: "OncoKB is a precision oncology knowledge base that annotates the biological consequences and clinical implications (therapeutic, diagnostic, and prognostic) of genetic variants in cancer. In order to use this you must provide a config file containing your own oncoKB api key in the args."
+      documentation: "https://github.com/oncokb/oncokb-annotator"
+      licence: ["GNU"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. `[ id:'sample1']`
+    - inputMaf:
+        type: file
+        description: MAF, perferrably annotated by vcf2maf. Required cols are listed in the docs.
+        pattern: "*.maf"
+output:
+  - oncokb_maf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1']`
+      - "*.oncokb.maf":
+          type: file
+          description: A maf file annotated by oncokb
+          pattern: "*.{maf}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@johnoooh"
+maintainers:
+  - "@johnoooh"
+

modules/msk/oncokb/mafannotate/tests/main.nf.test

@@ -0,0 +1,66 @@
+nextflow_process {
+
+    name "Test Process ONCOKB_MAFANNOTATE"
+    script "../main.nf"
+    process "ONCOKB_MAFANNOTATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "modules_msk"
+    tag "oncokb"
+    tag "oncokb/mafannotate"
+
+
+    test("test") {
+
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test',case_id:'sample1',control_id:'sample2'], // meta map
+                    file(params.test_data_mskcc['genome_nexus']['sample2_sample1_annotated_maf'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+
+            )
+        }
+
+    }
+
+
+    test("test normal - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+
+
+                input[0] = [
+                    [ id:'test',case_id:'sample1',control_id:'sample2'], // meta map
+                    file(params.test_data_mskcc['genome_nexus']['sample2_sample1_annotated_maf'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+
+            )
+        }
+
+    }
+
+}

modules/msk/oncokb/mafannotate/tests/main.nf.test.snap

@@ -0,0 +1,39 @@
+{
+    "test": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "case_id": "sample1",
+                            "control_id": "sample2"
+                        },
+                        "test.oncokb.maf:md5,dd58c4431ec26cb47fb97236d063c6a5"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,030d3dd4facf29936752666113de5897"
+                ],
+                "oncokb_maf": [
+                    [
+                        {
+                            "id": "test",
+                            "case_id": "sample1",
+                            "control_id": "sample2"
+                        },
+                        "test.oncokb.maf:md5,dd58c4431ec26cb47fb97236d063c6a5"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,030d3dd4facf29936752666113de5897"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2025-03-03T13:18:05.707580942"
+    }
+}

modules/msk/oncokb/mafannotate/tests/tags.yml

@@ -0,0 +1,2 @@
+genomenexus/annotationpipeline:
+  - "modules/msk/oncokb/mafannotate/**"