acela-cli modules

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

@@ -66,11 +66,17 @@ runs:
         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 != '' 
+      if: env.ONCOKB_TOKEN != ''
       shell: bash
       run: |
         nextflow secrets set ONCOKB_TOKEN $ONCOKB_TOKEN
 
+    - name: Set up nextflow ACELA secrets
+      # acela/bampatientid and acela/bamsampleid only run stub tests in CI (the Acela API is internal-only)
+      shell: bash
+      run: |
+        nextflow secrets set ACELA_TOKEN stub-placeholder
+
 
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017

.github/skip_nf_test.json

@@ -33,6 +33,8 @@
         "modules/msk/pvmaf/concat",
         "modules/msk/pvmaf/tagtraceback",
         "modules/msk/oncokb/mafannotate",
+        "modules/msk/acela/bampatientid",
+        "modules/msk/acela/bamsampleid",
         "subworkflows/msk/genome_nexus",
         "subworkflows/msk/netmhcstabandpan",
         "subworkflows/msk/phylowgs",

modules/msk/acela/bampatientid/environment.yml

@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # acela-cli is a private MSKCC package, not available on Bioconda/PyPI.
+  # Install it into the container image via:
+  #   pip install git+ssh://git@github.com/mskcc/acela-cli.git
+  - "YOUR-TOOL=HERE"

modules/msk/acela/bampatientid/main.nf

@@ -0,0 +1,58 @@
+process ACELA_BAMPATIENTID {
+    tag "$meta.id"
+    label 'process_single'
+
+    // acela-cli authenticates to the internal MSKCC Acela/Voyager API with a session token.
+    // Before running a pipeline that uses this module, obtain one (`acela login`)
+    secret 'ACELA_TOKEN'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/mskcc-omics-workflows/acela_cli:0.1.0-amd64':
+        'ghcr.io/mskcc-omics-workflows/acela_cli:0.1.0-amd64' }"
+
+    input:
+    tuple val(meta), val(patient_ids)
+
+    output:
+    tuple val(meta), path("*.acela_bam.tsv"), emit: tsv
+    path "versions.yml",                      emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if (!(meta.id_type in ['cmo', 'dmp'])) {
+        error "ACELA_BAMPATIENTID: meta.id_type must be 'cmo' or 'dmp', got '${meta.id_type}'"
+    }
+    def subcommand = meta.id_type == 'dmp' ? 'by-dmp-id' : 'by-cmo-id'
+    def ids = (patient_ids instanceof List ? patient_ids : [patient_ids]).join(' ')
+    def sep_arg = meta.sep ? "--sep '${meta.sep}'" : ''
+
+    """
+    acela bam ${subcommand} \\
+        ${ids} \\
+        --output ${prefix}.acela_bam.tsv \\
+        ${sep_arg} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        acela-cli: \$(echo \$(acela --version) | sed -e "s/acela-cli //g")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.acela_bam.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        acela-cli: \$(echo \$(acela --version) | sed -e "s/acela-cli //g")
+    END_VERSIONS
+    """
+}

modules/msk/acela/bampatientid/meta.yml

@@ -0,0 +1,52 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "acela_bampatientid"
+description: Look up mirrored BAM file paths and sample metadata by CMO or DMP patient ID using the Acela CLI.
+keywords:
+  - acela
+  - bam
+  - mirror
+  - mskcc
+tools:
+  - "acela-cli":
+      description: "Command-line client for the Acela BAM mirror API. Looks up BAM files by patient/sample ID and returns tab-delimited or JSON results. Requires network access to the internal MSKCC Acela/Voyager endpoint and a valid session token. Before running a pipeline that uses this module, obtain a token (`acela login`, or set ACELA_USER/ACELA_PASSWORD once) and register it locally with `nextflow secrets set ACELA_TOKEN <token>` -- Nextflow injects it into the task environment at runtime."
+      homepage: "https://github.com/mskcc/acela-cli"
+      documentation: "https://github.com/mskcc/acela-cli"
+      licence: ["unspecified (private MSKCC repository)"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information, plus an `id_type` key selecting which Acela
+          lookup to perform, and an optional `sep` key selecting the output field delimiter
+          ("tsv" (default), "csv", "\s" for space, or any literal character, e.g. "|").
+          e.g. `[ id:'patient1', id_type:'cmo' ]` or `[ id:'patient1', id_type:'dmp', sep:'csv' ]`
+    - patient_ids:
+        type: list
+        description: |
+          One or more patient identifiers to look up, matching `meta.id_type`: CMO patient IDs
+          (e.g. `C-ABCDEF`) when `id_type` is `cmo`, or DMP patient IDs (e.g. `P-0001234`) when
+          `id_type` is `dmp`. A single String is also accepted for a one-off lookup.
+output:
+  tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'patient1', id_type:'cmo' ]`
+      - "*.acela_bam.tsv":
+          type: file
+          description: Tab-delimited mirrored BAM paths and sample metadata returned by the Acela API.
+          pattern: "*.acela_bam.tsv"
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+authors:
+  - "@buehlere"
+maintainers:
+  - "@buehlere"

modules/msk/acela/bampatientid/tests/main.nf.test

@@ -0,0 +1,64 @@
+// nf-core modules test acela/bampatientid
+nextflow_process {
+
+    name "Test Process ACELA_BAMPATIENTID"
+    script "../main.nf"
+    process "ACELA_BAMPATIENTID"
+
+    tag "modules"
+    tag "modules_msk"
+    tag "acela"
+    tag "acela/bampatientid"
+
+    // acela-cli talks to a live, internal-only MSKCC endpoint and requires a real session
+    // token, so it cannot run against fixture data in CI. Stub-only test per the MSK
+    // contributing guide's allowance for modules that can't run on small test data.
+    test("cmo patient id - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'patient1', id_type:'cmo' ], // meta map
+                    ['C-ABCDEF', 'C-GHIJKL']
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("dmp patient id - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'patient2', id_type:'dmp' ], // meta map
+                    'P-0001234'
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/msk/acela/bampatientid/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "dmp patient id - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "patient2",
+                            "id_type": "dmp"
+                        },
+                        "patient2.acela_bam.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b92b4a337b21c1a5682425e69fcf0b20"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "patient2",
+                            "id_type": "dmp"
+                        },
+                        "patient2.acela_bam.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b92b4a337b21c1a5682425e69fcf0b20"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2026-08-14T10:34:19.513344"
+    },
+    "cmo patient id - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "patient1",
+                            "id_type": "cmo"
+                        },
+                        "patient1.acela_bam.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b92b4a337b21c1a5682425e69fcf0b20"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "patient1",
+                            "id_type": "cmo"
+                        },
+                        "patient1.acela_bam.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b92b4a337b21c1a5682425e69fcf0b20"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2026-08-14T10:34:15.706525"
+    }
+}

modules/msk/acela/bamsampleid/environment.yml

@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # acela-cli is a private MSKCC package, not available on Bioconda/PyPI.
+  # Install it into the container image via:
+  #   pip install git+ssh://git@github.com/mskcc/acela-cli.git
+  - "YOUR-TOOL=HERE"

modules/msk/acela/bamsampleid/main.nf

@@ -0,0 +1,53 @@
+process ACELA_BAMSAMPLEID {
+    tag "$meta.id"
+    label 'process_single'
+
+    // acela-cli authenticates to the internal MSKCC Acela/Voyager API with a session token.
+    // Before running a pipeline that uses this module, obtain one (`acela login`)
+    secret 'ACELA_TOKEN'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'ghcr.io/mskcc-omics-workflows/acela_cli:0.1.0-amd64':
+        'ghcr.io/mskcc-omics-workflows/acela_cli:0.1.0-amd64' }"
+
+    input:
+    tuple val(meta), val(dmp_sample_ids)
+
+    output:
+    tuple val(meta), path("*.acela_bam.tsv"), emit: tsv
+    path "versions.yml",                      emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def ids = (dmp_sample_ids instanceof List ? dmp_sample_ids : [dmp_sample_ids]).join(' ')
+    def sep_arg = meta.sep ? "--sep '${meta.sep}'" : ''
+
+    """
+    acela bam by-sample-id \\
+        ${ids} \\
+        --output ${prefix}.acela_bam.tsv \\
+        ${sep_arg} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        acela-cli: \$(echo \$(acela --version) | sed -e "s/acela-cli //g")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.acela_bam.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        acela-cli: \$(echo \$(acela --version) | sed -e "s/acela-cli //g")
+    END_VERSIONS
+    """
+}