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Merge branch 'develop' into module/fingerprintparser
2 parents 3cc109e + 89a7643 commit 70ffc3f

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‎.github/CODEOWNERS‎

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

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

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

‎.github/conda_skip.yml‎

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

‎.github/skip_nf_test.json‎

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"modules/msk/pvmaf/concat",
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"modules/msk/pvmaf/tagtraceback",
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"subworkflows/msk/fingerprint_gbcms",
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"subworkflows/msk/genome_nexus"
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"subworkflows/msk/genome_nexus",
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"modules/msk/oncokb/mafannotate"
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],
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"docker": [
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],

‎.github/workflows/nf-test.yml‎

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

‎modules/msk/oncokb/mafannotate/environment.yml‎

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

‎modules/msk/oncokb/mafannotate/main.nf‎

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

‎modules/msk/oncokb/mafannotate/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "oncokb_mafannotate"
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description:
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Takes a Maf and annotates it using OncoKB.
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keywords:
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- oncokb
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- maf
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- annotation
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tools:
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- oncokb:
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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."
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documentation: "https://github.com/oncokb/oncokb-annotator"
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licence: ["GNU"]
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identifier: ""
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information.
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e.g. `[ id:'sample1']`
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- inputMaf:
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type: file
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description: MAF, perferrably annotated by vcf2maf. Required cols are listed in the docs.
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pattern: "*.maf"
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output:
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- oncokb_maf:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1']`
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- "*.oncokb.maf":
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type: file
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description: A maf file annotated by oncokb
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pattern: "*.{maf}"
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- versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@johnoooh"
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maintainers:
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- "@johnoooh"
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‎modules/msk/oncokb/mafannotate/tests/main.nf.test‎

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

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

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

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