New module - TD2 (added modules for td2.longorfs & td2.predict)

modules/nf-core/td2/longorfs/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::td2=1.0.6"

modules/nf-core/td2/longorfs/main.nf

@@ -0,0 +1,43 @@
+process TD2_LONGORFS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/41/4155bf3b720e1e32d0615a947696fb0287ee4e8cdbeb4ec784dd4da7bb5b2e86/data':
+        "community.wave.seqera.io/library/td2:1.0.6--ea3e5ac09443b677"}"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("${prefix}/longest_orfs.{cds,gff3,pep}"), emit: orfs
+    tuple val("${task.process}"), val('TD2.LongOrfs'), eval("echo ${VERSION}"), emit: versions_td2, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    VERSION = '1.0.6' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    TD2.LongOrfs \\
+    -t ${fasta} \\
+    -O ${prefix} \\
+    --threads ${task.cpus} \\
+    ${args}
+    """
+
+    stub:
+    VERSION = 'v1.0.6' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}/
+    touch ${prefix}/longest_orfs.cds
+    touch ${prefix}/longest_orfs.gff3
+    touch ${prefix}/longest_orfs.pep
+    """
+}

modules/nf-core/td2/longorfs/meta.yml

@@ -0,0 +1,71 @@
+name: "td2_longorfs"
+description: TD2 identifies candidate coding regions within transcript
+  sequences, such as those generated by de novo RNA-Seq transcript assembly
+keywords:
+  - td2
+  - orfs
+  - longorfs
+  - transcripts
+tools:
+  - td2:
+      description: "TD2 identifies candidate coding regions within transcript sequences,
+        such as those generated by de novo RNA-Seq transcript assembly"
+      homepage: "https://github.com/Markusjsommer/TD2"
+      documentation: "https://github.com/Markusjsommer/TD2"
+      tool_dev_url: "https://github.com/Markusjsommer/TD2"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: Fasta file containing the target transcript sequences
+        pattern: "*.{fasta}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
+output:
+  orfs:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}/longest_orfs.{cds,gff3,pep}:
+          type: file
+          description: Files containing the longest ORFs predicted from the input
+            transcript sequences
+          pattern: "${prefix}/longest_orfs.{cds,gff3,pep}"
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
+            - edam: http://edamontology.org/format_1975 # GFF3
+            - edam: http://edamontology.org/format_1960 # Protein FASTA
+  versions_td2:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - TD2.LongOrfs:
+          type: string
+          description: The tool name
+      - echo ${VERSION}:
+          type: string
+          description: The tool version
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - TD2.LongOrfs:
+          type: string
+          description: The tool name
+      - echo ${VERSION}:
+          type: string
+          description: The tool version
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"

modules/nf-core/td2/longorfs/tests/main.nf.test

@@ -0,0 +1,64 @@
+nextflow_process {
+
+    name "Test Process TD2_LONGORFS"
+    script "../main.nf"
+    process "TD2_LONGORFS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "td2"
+    tag "td2/longorfs"
+
+    test("td2.longorfs - transcriptome.fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_td2_longorfs' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out.orfs,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+            )
+        }
+
+    }
+
+    test("td2.longorfs - transcriptome.fasta -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_td2_longorfs' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out.orfs,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/td2/longorfs/tests/main.nf.test.snap

@@ -0,0 +1,62 @@
+{
+    "td2.longorfs - transcriptome.fasta": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_td2_longorfs"
+                    },
+                    [
+                        "longest_orfs.cds:md5,4226fe196a4527f938e25061ffe7eaf6",
+                        "longest_orfs.gff3:md5,864ae9147b65d07eb9d79c0e42968e12",
+                        "longest_orfs.pep:md5,0151dac6998be924139a4f5a5a0c590b"
+                    ]
+                ]
+            ],
+            {
+                "versions_td2": [
+                    [
+                        "TD2_LONGORFS",
+                        "TD2.LongOrfs",
+                        "1.0.6"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-08T22:55:17.67412706"
+    },
+    "td2.longorfs - transcriptome.fasta -stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_td2_longorfs"
+                    },
+                    [
+                        "longest_orfs.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "longest_orfs.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "longest_orfs.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            ],
+            {
+                "versions_td2": [
+                    [
+                        "TD2_LONGORFS",
+                        "TD2.LongOrfs",
+                        "1.0.6"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-08T22:57:07.433423015"
+    }
+}

modules/nf-core/td2/predict/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::td2=1.0.6"

modules/nf-core/td2/predict/main.nf

@@ -0,0 +1,47 @@
+process TD2_PREDICT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/41/4155bf3b720e1e32d0615a947696fb0287ee4e8cdbeb4ec784dd4da7bb5b2e86/data':
+        "community.wave.seqera.io/library/td2:1.0.6--ea3e5ac09443b677"}"
+
+    input:
+    tuple val(meta), path(fasta), path(orfs_dir, stageAs: 'orfs')
+
+    output:
+    tuple val(meta), path("${prefix}/*.TD2.{bed,cds,gff3,pep}")        , emit: predictions
+    tuple val("${task.process}"), val('TD2.Predict'), eval("echo ${VERSION}"), emit: versions_td2, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    VERSION = '1.0.6' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}/
+
+    TD2.Predict \\
+        -t ${fasta} \\
+        -O ${orfs_dir} \\
+        ${args}
+
+    mv *.TD2.{bed,cds,gff3,pep} ${prefix}/
+    """
+
+    stub:
+    VERSION = 'v1.0.6' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}/
+    touch ${prefix}/${fasta}.TD2.bed
+    touch ${prefix}/${fasta}.TD2.cds
+    touch ${prefix}/${fasta}.TD2.gff3
+    touch ${prefix}/${fasta}.TD2.pep
+    """
+}

modules/nf-core/td2/predict/meta.yml

@@ -0,0 +1,77 @@
+name: "td2_predict"
+description: TD2 identifies candidate coding regions within transcript
+  sequences, such as those generated by de novo RNA-Seq transcript assembly
+keywords:
+  - predict
+  - orfs
+  - coding regions
+  - td2.predict
+tools:
+  - "td2":
+      description: "TD2 identifies candidate coding regions within transcript sequences,
+        such as those generated by de novo RNA-Seq transcript assembly"
+      homepage: "https://github.com/Markusjsommer/TD2"
+      documentation: "https://github.com/Markusjsommer/TD2"
+      tool_dev_url: "https://github.com/Markusjsommer/TD2"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: Transcripts fasta file
+        pattern: "*.fasta"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
+    - orfs_dir:
+        type: file
+        description: Directory containing the ORF prediction files generated by
+          the `td2_longorfs` module
+        pattern: "orfs_dir/"
+        ontologies: []
+output:
+  predictions:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}/*.TD2.{bed,cds,gff3,pep}:
+          type: file
+          description: Files containing the TD2 ORF predictions for the input
+            transcript sequences
+          pattern: "${prefix}/*.TD2.{bed,cds,gff3,pep}"
+          ontologies:
+            - edam: http://edamontology.org/format_3003 # BED
+            - edam: http://edamontology.org/format_1929 # FASTA
+            - edam: http://edamontology.org/format_1975 # GFF3
+  versions_td2:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - TD2.Predict:
+          type: string
+          description: The tool name
+      - echo ${VERSION}:
+          type: string
+          description: The tool version
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - TD2.Predict:
+          type: string
+          description: The tool name
+      - echo ${VERSION}:
+          type: string
+          description: The tool version
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"