From f20472f8b57635a43a4a190a9a22febd5cc9beb5 Mon Sep 17 00:00:00 2001
From: khersameesh24 <khersameesh24@gmail.com>
Date: Fri, 28 Nov 2025 12:41:27 +0100
Subject: [PATCH 01/18] added modules for td2.longorfs & td2.predict

---
 modules/nf-core/td2/longorfs/environment.yml  |  5 +
 modules/nf-core/td2/longorfs/main.nf          | 51 ++++++++++
 modules/nf-core/td2/longorfs/meta.yml         | 54 ++++++++++
 .../nf-core/td2/longorfs/tests/main.nf.test   | 64 ++++++++++++
 .../td2/longorfs/tests/main.nf.test.snap      | 94 ++++++++++++++++++
 modules/nf-core/td2/predict/environment.yml   |  5 +
 modules/nf-core/td2/predict/main.nf           | 55 +++++++++++
 modules/nf-core/td2/predict/meta.yml          | 58 +++++++++++
 .../nf-core/td2/predict/tests/main.nf.test    | 79 +++++++++++++++
 .../td2/predict/tests/main.nf.test.snap       | 98 +++++++++++++++++++
 10 files changed, 563 insertions(+)
 create mode 100644 modules/nf-core/td2/longorfs/environment.yml
 create mode 100644 modules/nf-core/td2/longorfs/main.nf
 create mode 100644 modules/nf-core/td2/longorfs/meta.yml
 create mode 100644 modules/nf-core/td2/longorfs/tests/main.nf.test
 create mode 100644 modules/nf-core/td2/longorfs/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/td2/predict/environment.yml
 create mode 100644 modules/nf-core/td2/predict/main.nf
 create mode 100644 modules/nf-core/td2/predict/meta.yml
 create mode 100644 modules/nf-core/td2/predict/tests/main.nf.test
 create mode 100644 modules/nf-core/td2/predict/tests/main.nf.test.snap

diff --git a/modules/nf-core/td2/longorfs/environment.yml b/modules/nf-core/td2/longorfs/environment.yml
new file mode 100644
index 000000000000..db97153a88db
--- /dev/null
+++ b/modules/nf-core/td2/longorfs/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::td2=1.0.6"
diff --git a/modules/nf-core/td2/longorfs/main.nf b/modules/nf-core/td2/longorfs/main.nf
new file mode 100644
index 000000000000..150f60fe26c4
--- /dev/null
+++ b/modules/nf-core/td2/longorfs/main.nf
@@ -0,0 +1,51 @@
+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
+    path("versions.yml")                                          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    TD2.LongOrfs \\
+    -t ${fasta} \\
+    -O ${prefix} \\
+    --threads ${task.cpus} \\
+    ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        td2: \$(td2 v1.0.6)
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}/
+    touch ${prefix}/longest_orfs.cds
+    touch ${prefix}/longest_orfs.gff3
+    touch ${prefix}/longest_orfs.pep
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        td2: \$(td2 v1.0.6)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/td2/longorfs/meta.yml b/modules/nf-core/td2/longorfs/meta.yml
new file mode 100644
index 000000000000..a5bd03180502
--- /dev/null
+++ b/modules/nf-core/td2/longorfs/meta.yml
@@ -0,0 +1,54 @@
+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: []
+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: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"
diff --git a/modules/nf-core/td2/longorfs/tests/main.nf.test b/modules/nf-core/td2/longorfs/tests/main.nf.test
new file mode 100644
index 000000000000..6573d4c5998a
--- /dev/null
+++ b/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,
+                    path(process.out.versions[0]).yaml
+                ).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,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/td2/longorfs/tests/main.nf.test.snap b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
new file mode 100644
index 000000000000..3203bb436031
--- /dev/null
+++ b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
@@ -0,0 +1,94 @@
+{
+    "td2.longorfs - transcriptome.fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_td2_longorfs"
+                        },
+                        [
+                            "longest_orfs.cds:md5,4226fe196a4527f938e25061ffe7eaf6",
+                            "longest_orfs.gff3:md5,864ae9147b65d07eb9d79c0e42968e12",
+                            "longest_orfs.pep:md5,0151dac6998be924139a4f5a5a0c590b"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0856a2e8d28b454f9c3a768cd3451f1a"
+                ],
+                "orfs": [
+                    [
+                        {
+                            "id": "test_td2_longorfs"
+                        },
+                        [
+                            "longest_orfs.cds:md5,4226fe196a4527f938e25061ffe7eaf6",
+                            "longest_orfs.gff3:md5,864ae9147b65d07eb9d79c0e42968e12",
+                            "longest_orfs.pep:md5,0151dac6998be924139a4f5a5a0c590b"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0856a2e8d28b454f9c3a768cd3451f1a"
+                ]
+            },
+            {
+                "TD2_LONGORFS": {
+                    "td2": null
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-27T09:33:10.428948889"
+    },
+    "td2.longorfs - transcriptome.fasta -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_td2_longorfs"
+                        },
+                        [
+                            "longest_orfs.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "longest_orfs.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "longest_orfs.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0856a2e8d28b454f9c3a768cd3451f1a"
+                ],
+                "orfs": [
+                    [
+                        {
+                            "id": "test_td2_longorfs"
+                        },
+                        [
+                            "longest_orfs.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "longest_orfs.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "longest_orfs.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0856a2e8d28b454f9c3a768cd3451f1a"
+                ]
+            },
+            {
+                "TD2_LONGORFS": {
+                    "td2": null
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-27T09:35:15.301277063"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/td2/predict/environment.yml b/modules/nf-core/td2/predict/environment.yml
new file mode 100644
index 000000000000..db97153a88db
--- /dev/null
+++ b/modules/nf-core/td2/predict/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::td2=1.0.6"
diff --git a/modules/nf-core/td2/predict/main.nf b/modules/nf-core/td2/predict/main.nf
new file mode 100644
index 000000000000..866f06f6a96a
--- /dev/null
+++ b/modules/nf-core/td2/predict/main.nf
@@ -0,0 +1,55 @@
+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
+    path("versions.yml")                                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}/
+
+    TD2.Predict \\
+        -t ${fasta} \\
+        -O ${orfs_dir} \\
+        ${args}
+
+    mv *.TD2.{bed,cds,gff3,pep} ${prefix}/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        td2: \$(td2 v1.0.6)
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}/
+    touch ${prefix}/fakefile.TD2.bed
+    touch ${prefix}/fakefile.TD2.cds
+    touch ${prefix}/fakefile.TD2.gff3
+    touch ${prefix}/fakefile.TD2.pep
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        td2: \$(td2 v1.0.6)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/td2/predict/meta.yml b/modules/nf-core/td2/predict/meta.yml
new file mode 100644
index 000000000000..bdf8b0f6d3c4
--- /dev/null
+++ b/modules/nf-core/td2/predict/meta.yml
@@ -0,0 +1,58 @@
+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: []
+    - 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: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"
diff --git a/modules/nf-core/td2/predict/tests/main.nf.test b/modules/nf-core/td2/predict/tests/main.nf.test
new file mode 100644
index 000000000000..069768124443
--- /dev/null
+++ b/modules/nf-core/td2/predict/tests/main.nf.test
@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process TD2_PREDICT"
+    script "../main.nf"
+    process "TD2_PREDICT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "td2"
+    tag "td2/longorfs"
+    tag "td2/predict"
+
+    setup {
+        run("TD2_LONGORFS") {
+            script "modules/nf-core/td2/longorfs/main.nf"
+            process {
+                """
+                input[0] = [
+                    [id:'test_td2_predict'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("td2.predict - transcriptome.fasta") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test_td2_predict'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]).combine(TD2_LONGORFS.out.orfs.map{ meta, orfs -> return [meta, file(orfs[0].getParent())] }, by: 0)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+
+    }
+
+    test("td2.predict - transcriptome.fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test_td2_predict'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]).combine(TD2_LONGORFS.out.orfs.map{ meta, orfs -> return [meta, file(orfs[0].getParent())] }, by: 0)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/td2/predict/tests/main.nf.test.snap b/modules/nf-core/td2/predict/tests/main.nf.test.snap
new file mode 100644
index 000000000000..d788b3e1ef67
--- /dev/null
+++ b/modules/nf-core/td2/predict/tests/main.nf.test.snap
@@ -0,0 +1,98 @@
+{
+    "td2.predict - transcriptome.fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_td2_predict"
+                        },
+                        [
+                            "genome.fasta.TD2.bed:md5,2504559bdf4e321bc0612573be0a1eb6",
+                            "genome.fasta.TD2.cds:md5,e3f601c2ab4e9513b6577bbcdc19fda5",
+                            "genome.fasta.TD2.gff3:md5,0e4fd0095da808937192caee48fe47d5",
+                            "genome.fasta.TD2.pep:md5,390c241ee523756f3cd81b3cf2fa62ac"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,20f64996cc943420260fa0be53c2ff71"
+                ],
+                "predictions": [
+                    [
+                        {
+                            "id": "test_td2_predict"
+                        },
+                        [
+                            "genome.fasta.TD2.bed:md5,2504559bdf4e321bc0612573be0a1eb6",
+                            "genome.fasta.TD2.cds:md5,e3f601c2ab4e9513b6577bbcdc19fda5",
+                            "genome.fasta.TD2.gff3:md5,0e4fd0095da808937192caee48fe47d5",
+                            "genome.fasta.TD2.pep:md5,390c241ee523756f3cd81b3cf2fa62ac"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,20f64996cc943420260fa0be53c2ff71"
+                ]
+            },
+            {
+                "TD2_PREDICT": {
+                    "td2": null
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-28T12:34:19.705175228"
+    },
+    "td2.predict - transcriptome.fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_td2_predict"
+                        },
+                        [
+                            "fakefile.TD2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "fakefile.TD2.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "fakefile.TD2.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "fakefile.TD2.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,20f64996cc943420260fa0be53c2ff71"
+                ],
+                "predictions": [
+                    [
+                        {
+                            "id": "test_td2_predict"
+                        },
+                        [
+                            "fakefile.TD2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "fakefile.TD2.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "fakefile.TD2.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "fakefile.TD2.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,20f64996cc943420260fa0be53c2ff71"
+                ]
+            },
+            {
+                "TD2_PREDICT": {
+                    "td2": null
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-27T12:57:15.490423827"
+    }
+}
\ No newline at end of file

From 74fea509012fa3c39bbae310a487db989e3b8810 Mon Sep 17 00:00:00 2001
From: khersameesh24 <khersameesh24@gmail.com>
Date: Thu, 4 Dec 2025 21:39:04 +0100
Subject: [PATCH 02/18] changes to version handling, updated snaps, and tests -
 resolving comments

---
 modules/nf-core/td2/longorfs/main.nf          | 14 +----
 modules/nf-core/td2/longorfs/meta.yml         | 18 +++---
 .../nf-core/td2/longorfs/tests/main.nf.test   |  4 +-
 .../td2/longorfs/tests/main.nf.test.snap      | 56 +++++++++++++------
 modules/nf-core/td2/predict/main.nf           | 14 +----
 modules/nf-core/td2/predict/meta.yml          | 24 ++++----
 .../nf-core/td2/predict/tests/main.nf.test    |  4 +-
 .../td2/predict/tests/main.nf.test.snap       | 56 +++++++++++++------
 8 files changed, 114 insertions(+), 76 deletions(-)

diff --git a/modules/nf-core/td2/longorfs/main.nf b/modules/nf-core/td2/longorfs/main.nf
index 150f60fe26c4..bf6e9f389dab 100644
--- a/modules/nf-core/td2/longorfs/main.nf
+++ b/modules/nf-core/td2/longorfs/main.nf
@@ -12,13 +12,14 @@ process TD2_LONGORFS {
 
     output:
     tuple val(meta), path("${prefix}/longest_orfs.{cds,gff3,pep}"), emit: orfs
-    path("versions.yml")                                          , emit: versions
+    tuple val("${task.process}"), val('TD2.LongOrfs'), eval("echo td2: ${VERSION}"), emit: versions_td2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    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}"
 
     """
@@ -27,14 +28,10 @@ process TD2_LONGORFS {
     -O ${prefix} \\
     --threads ${task.cpus} \\
     ${args}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        td2: \$(td2 v1.0.6)
-    END_VERSIONS
     """
 
     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}"
 
     """
@@ -42,10 +39,5 @@ process TD2_LONGORFS {
     touch ${prefix}/longest_orfs.cds
     touch ${prefix}/longest_orfs.gff3
     touch ${prefix}/longest_orfs.pep
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        td2: \$(td2 v1.0.6)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/td2/longorfs/meta.yml b/modules/nf-core/td2/longorfs/meta.yml
index a5bd03180502..183dfef95850 100644
--- a/modules/nf-core/td2/longorfs/meta.yml
+++ b/modules/nf-core/td2/longorfs/meta.yml
@@ -40,14 +40,16 @@ output:
             transcript sequences
           pattern: "${prefix}/longest_orfs.{cds,gff3,pep}"
           ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: "http://edamontology.org/format_3750" # YAML
-
+  versions_td2:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - TD2.LongOrfs:
+          type: string
+          description: The tool name
+      - "echo td2: ${VERSION}":
+          type: string
+          description: The version of TD2 used
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/modules/nf-core/td2/longorfs/tests/main.nf.test b/modules/nf-core/td2/longorfs/tests/main.nf.test
index 6573d4c5998a..9f76f25c345e 100644
--- a/modules/nf-core/td2/longorfs/tests/main.nf.test
+++ b/modules/nf-core/td2/longorfs/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     process.out,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
         }
@@ -54,7 +54,7 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     process.out,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
         }
diff --git a/modules/nf-core/td2/longorfs/tests/main.nf.test.snap b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
index 3203bb436031..aa8376128b76 100644
--- a/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
+++ b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
@@ -15,7 +15,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0856a2e8d28b454f9c3a768cd3451f1a"
+                    [
+                        "TD2_LONGORFS",
+                        "TD2.LongOrfs",
+                        "td2: v1.0.6"
+                    ]
                 ],
                 "orfs": [
                     [
@@ -29,21 +33,29 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,0856a2e8d28b454f9c3a768cd3451f1a"
+                "versions_td2": [
+                    [
+                        "TD2_LONGORFS",
+                        "TD2.LongOrfs",
+                        "td2: v1.0.6"
+                    ]
                 ]
             },
             {
-                "TD2_LONGORFS": {
-                    "td2": null
-                }
+                "versions_td2": [
+                    [
+                        "TD2_LONGORFS",
+                        "TD2.LongOrfs",
+                        "td2: v1.0.6"
+                    ]
+                ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-27T09:33:10.428948889"
+        "timestamp": "2025-12-04T21:11:35.499924547"
     },
     "td2.longorfs - transcriptome.fasta -stub": {
         "content": [
@@ -61,7 +73,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0856a2e8d28b454f9c3a768cd3451f1a"
+                    [
+                        "TD2_LONGORFS",
+                        "TD2.LongOrfs",
+                        "td2: v1.0.6"
+                    ]
                 ],
                 "orfs": [
                     [
@@ -75,20 +91,28 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,0856a2e8d28b454f9c3a768cd3451f1a"
+                "versions_td2": [
+                    [
+                        "TD2_LONGORFS",
+                        "TD2.LongOrfs",
+                        "td2: v1.0.6"
+                    ]
                 ]
             },
             {
-                "TD2_LONGORFS": {
-                    "td2": null
-                }
+                "versions_td2": [
+                    [
+                        "TD2_LONGORFS",
+                        "TD2.LongOrfs",
+                        "td2: v1.0.6"
+                    ]
+                ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-27T09:35:15.301277063"
+        "timestamp": "2025-12-04T21:13:55.06359889"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/td2/predict/main.nf b/modules/nf-core/td2/predict/main.nf
index 866f06f6a96a..78a444d6d4d3 100644
--- a/modules/nf-core/td2/predict/main.nf
+++ b/modules/nf-core/td2/predict/main.nf
@@ -12,13 +12,14 @@ process TD2_PREDICT {
 
     output:
     tuple val(meta), path("${prefix}/*.TD2.{bed,cds,gff3,pep}"), emit: predictions
-    path("versions.yml")                                       , emit: versions
+    tuple val("${task.process}"), val('TD2.Predict'), eval("echo td2: ${VERSION}"), emit: versions_td2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    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}"
 
     """
@@ -30,14 +31,10 @@ process TD2_PREDICT {
         ${args}
 
     mv *.TD2.{bed,cds,gff3,pep} ${prefix}/
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        td2: \$(td2 v1.0.6)
-    END_VERSIONS
     """
 
     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}"
 
     """
@@ -46,10 +43,5 @@ process TD2_PREDICT {
     touch ${prefix}/fakefile.TD2.cds
     touch ${prefix}/fakefile.TD2.gff3
     touch ${prefix}/fakefile.TD2.pep
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        td2: \$(td2 v1.0.6)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/td2/predict/meta.yml b/modules/nf-core/td2/predict/meta.yml
index bdf8b0f6d3c4..a38895035943 100644
--- a/modules/nf-core/td2/predict/meta.yml
+++ b/modules/nf-core/td2/predict/meta.yml
@@ -29,7 +29,8 @@ input:
         ontologies: []
     - orfs_dir:
         type: file
-        description: Directory containing the ORF prediction files generated by the `td2_longorfs` module
+        description: Directory containing the ORF prediction files generated by
+          the `td2_longorfs` module
         pattern: "orfs_dir/"
         ontologies: []
 output:
@@ -41,17 +42,20 @@ output:
             e.g. `[ id:'sample1' ]`
       - ${prefix}/*.TD2.{bed,cds,gff3,pep}:
           type: file
-          description: Files containing the TD2 ORF predictions for the input transcript sequences
+          description: Files containing the TD2 ORF predictions for the input
+            transcript sequences
           pattern: "${prefix}/*.TD2.{bed,cds,gff3,pep}"
           ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: "http://edamontology.org/format_3750" # YAML
-
+  versions_td2:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - TD2.Predict:
+          type: string
+          description: The tool name
+      - "echo td2: ${VERSION}":
+          type: string
+          description: The version of TD2 used
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/modules/nf-core/td2/predict/tests/main.nf.test b/modules/nf-core/td2/predict/tests/main.nf.test
index 069768124443..4f3bb30eda27 100644
--- a/modules/nf-core/td2/predict/tests/main.nf.test
+++ b/modules/nf-core/td2/predict/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     process.out,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
         }
@@ -69,7 +69,7 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     process.out,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
         }
diff --git a/modules/nf-core/td2/predict/tests/main.nf.test.snap b/modules/nf-core/td2/predict/tests/main.nf.test.snap
index d788b3e1ef67..d366015e16a2 100644
--- a/modules/nf-core/td2/predict/tests/main.nf.test.snap
+++ b/modules/nf-core/td2/predict/tests/main.nf.test.snap
@@ -16,7 +16,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,20f64996cc943420260fa0be53c2ff71"
+                    [
+                        "TD2_PREDICT",
+                        "TD2.Predict",
+                        "td2: v1.0.6"
+                    ]
                 ],
                 "predictions": [
                     [
@@ -31,21 +35,29 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,20f64996cc943420260fa0be53c2ff71"
+                "versions_td2": [
+                    [
+                        "TD2_PREDICT",
+                        "TD2.Predict",
+                        "td2: v1.0.6"
+                    ]
                 ]
             },
             {
-                "TD2_PREDICT": {
-                    "td2": null
-                }
+                "versions_td2": [
+                    [
+                        "TD2_PREDICT",
+                        "TD2.Predict",
+                        "td2: v1.0.6"
+                    ]
+                ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-28T12:34:19.705175228"
+        "timestamp": "2025-12-04T21:17:11.987007488"
     },
     "td2.predict - transcriptome.fasta - stub": {
         "content": [
@@ -64,7 +76,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,20f64996cc943420260fa0be53c2ff71"
+                    [
+                        "TD2_PREDICT",
+                        "TD2.Predict",
+                        "td2: v1.0.6"
+                    ]
                 ],
                 "predictions": [
                     [
@@ -79,20 +95,28 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,20f64996cc943420260fa0be53c2ff71"
+                "versions_td2": [
+                    [
+                        "TD2_PREDICT",
+                        "TD2.Predict",
+                        "td2: v1.0.6"
+                    ]
                 ]
             },
             {
-                "TD2_PREDICT": {
-                    "td2": null
-                }
+                "versions_td2": [
+                    [
+                        "TD2_PREDICT",
+                        "TD2.Predict",
+                        "td2: v1.0.6"
+                    ]
+                ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-27T12:57:15.490423827"
+        "timestamp": "2025-12-04T21:19:34.49914593"
     }
 }
\ No newline at end of file

From b1d83fe5621a85453fa369d95aae75b43873ca9b Mon Sep 17 00:00:00 2001
From: khersameesh24 <khersameesh24@gmail.com>
Date: Thu, 4 Dec 2025 22:49:17 +0100
Subject: [PATCH 03/18] added topics section in meta.yml

---
 modules/nf-core/td2/longorfs/meta.yml | 11 +++++++++++
 modules/nf-core/td2/predict/meta.yml  | 11 +++++++++++
 2 files changed, 22 insertions(+)

diff --git a/modules/nf-core/td2/longorfs/meta.yml b/modules/nf-core/td2/longorfs/meta.yml
index 183dfef95850..b3052e387511 100644
--- a/modules/nf-core/td2/longorfs/meta.yml
+++ b/modules/nf-core/td2/longorfs/meta.yml
@@ -50,6 +50,17 @@ output:
       - "echo td2: ${VERSION}":
           type: string
           description: The version of TD2 used
+  topics:
+    - versions:
+        - - process:
+              type: string
+              description: The process the versions were collected from
+          - tool:
+              type: string
+              description: The tool name
+          - version:
+              type: string
+              description: The version of the tool
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/modules/nf-core/td2/predict/meta.yml b/modules/nf-core/td2/predict/meta.yml
index a38895035943..8dcf42f58638 100644
--- a/modules/nf-core/td2/predict/meta.yml
+++ b/modules/nf-core/td2/predict/meta.yml
@@ -56,6 +56,17 @@ output:
       - "echo td2: ${VERSION}":
           type: string
           description: The version of TD2 used
+  topics:
+    - versions:
+        - - process:
+              type: string
+              description: The process the versions were collected from
+          - tool:
+              type: string
+              description: The tool name
+          - version:
+              type: string
+              description: The version of the tool
 authors:
   - "@khersameesh24"
 maintainers:

From 9c4ba6e2811f1e2d9e43d4554f7e7e70fce25900 Mon Sep 17 00:00:00 2001
From: khersameesh24 <khersameesh24@gmail.com>
Date: Thu, 4 Dec 2025 23:17:49 +0100
Subject: [PATCH 04/18] fix topics section in meta.yml

---
 modules/nf-core/td2/longorfs/meta.yml | 22 +++++++++++-----------
 modules/nf-core/td2/predict/meta.yml  | 22 +++++++++++-----------
 2 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/modules/nf-core/td2/longorfs/meta.yml b/modules/nf-core/td2/longorfs/meta.yml
index b3052e387511..7ddeedfb29ab 100644
--- a/modules/nf-core/td2/longorfs/meta.yml
+++ b/modules/nf-core/td2/longorfs/meta.yml
@@ -50,17 +50,17 @@ output:
       - "echo td2: ${VERSION}":
           type: string
           description: The version of TD2 used
-  topics:
-    - versions:
-        - - process:
-              type: string
-              description: The process the versions were collected from
-          - tool:
-              type: string
-              description: The tool name
-          - version:
-              type: string
-              description: The version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - TD2.LongOrfs:
+          type: string
+          description: The tool name
+      - "echo td2: ${VERSION}":
+          type: string
+          description: The version of TD2 used
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/modules/nf-core/td2/predict/meta.yml b/modules/nf-core/td2/predict/meta.yml
index 8dcf42f58638..43bdbb5f71c1 100644
--- a/modules/nf-core/td2/predict/meta.yml
+++ b/modules/nf-core/td2/predict/meta.yml
@@ -56,17 +56,17 @@ output:
       - "echo td2: ${VERSION}":
           type: string
           description: The version of TD2 used
-  topics:
-    - versions:
-        - - process:
-              type: string
-              description: The process the versions were collected from
-          - tool:
-              type: string
-              description: The tool name
-          - version:
-              type: string
-              description: The version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - TD2.Predict:
+          type: string
+          description: The tool name
+      - "echo td2: ${VERSION}":
+          type: string
+          description: The version of TD2 used
 authors:
   - "@khersameesh24"
 maintainers:

From f0a0da8402b9f82bc21f343254e07765c326666e Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Mon, 8 Dec 2025 18:13:21 +0100
Subject: [PATCH 05/18] Update modules/nf-core/td2/longorfs/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/td2/longorfs/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/longorfs/main.nf b/modules/nf-core/td2/longorfs/main.nf
index bf6e9f389dab..3c61a865c37a 100644
--- a/modules/nf-core/td2/longorfs/main.nf
+++ b/modules/nf-core/td2/longorfs/main.nf
@@ -12,7 +12,7 @@ process TD2_LONGORFS {
 
     output:
     tuple val(meta), path("${prefix}/longest_orfs.{cds,gff3,pep}"), emit: orfs
-    tuple val("${task.process}"), val('TD2.LongOrfs'), eval("echo td2: ${VERSION}"), emit: versions_td2, topic: versions
+    tuple val("${task.process}"), val('TD2.LongOrfs'), eval("echo ${VERSION}"), emit: versions_td2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

From f97550061148175044e4840fc4c9d2acd0a7827c Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Mon, 8 Dec 2025 18:13:36 +0100
Subject: [PATCH 06/18] Update modules/nf-core/td2/longorfs/meta.yml

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/td2/longorfs/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/longorfs/meta.yml b/modules/nf-core/td2/longorfs/meta.yml
index 7ddeedfb29ab..159b5486c510 100644
--- a/modules/nf-core/td2/longorfs/meta.yml
+++ b/modules/nf-core/td2/longorfs/meta.yml
@@ -58,7 +58,7 @@ topics:
       - TD2.LongOrfs:
           type: string
           description: The tool name
-      - "echo td2: ${VERSION}":
+      - "echo ${VERSION}":
           type: string
           description: The version of TD2 used
 authors:

From ad4fab131b405e685294f3c41085999030df505e Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Mon, 8 Dec 2025 18:13:50 +0100
Subject: [PATCH 07/18] Update modules/nf-core/td2/predict/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/td2/predict/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/predict/main.nf b/modules/nf-core/td2/predict/main.nf
index 78a444d6d4d3..e824cdb89585 100644
--- a/modules/nf-core/td2/predict/main.nf
+++ b/modules/nf-core/td2/predict/main.nf
@@ -12,7 +12,7 @@ process TD2_PREDICT {
 
     output:
     tuple val(meta), path("${prefix}/*.TD2.{bed,cds,gff3,pep}"), emit: predictions
-    tuple val("${task.process}"), val('TD2.Predict'), eval("echo td2: ${VERSION}"), emit: versions_td2, topic: versions
+    tuple val("${task.process}"), val('TD2.Predict'), eval("echo ${VERSION}"), emit: versions_td2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

From ffdb366e8d2f93056ba01114af6b5341f2fc48ff Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Mon, 8 Dec 2025 18:14:06 +0100
Subject: [PATCH 08/18] Update modules/nf-core/td2/longorfs/meta.yml

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/td2/longorfs/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/longorfs/meta.yml b/modules/nf-core/td2/longorfs/meta.yml
index 159b5486c510..21607838e7ee 100644
--- a/modules/nf-core/td2/longorfs/meta.yml
+++ b/modules/nf-core/td2/longorfs/meta.yml
@@ -47,7 +47,7 @@ output:
       - TD2.LongOrfs:
           type: string
           description: The tool name
-      - "echo td2: ${VERSION}":
+      - "echo ${VERSION}":
           type: string
           description: The version of TD2 used
 topics:

From 551073e59e57efe214ce32f6b8a8a1f4e8e5e7a9 Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Mon, 8 Dec 2025 18:16:13 +0100
Subject: [PATCH 09/18] Update main.nf - stub run

---
 modules/nf-core/td2/predict/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/td2/predict/main.nf b/modules/nf-core/td2/predict/main.nf
index e824cdb89585..b83fddb182f8 100644
--- a/modules/nf-core/td2/predict/main.nf
+++ b/modules/nf-core/td2/predict/main.nf
@@ -39,9 +39,9 @@ process TD2_PREDICT {
 
     """
     mkdir -p ${prefix}/
-    touch ${prefix}/fakefile.TD2.bed
-    touch ${prefix}/fakefile.TD2.cds
-    touch ${prefix}/fakefile.TD2.gff3
-    touch ${prefix}/fakefile.TD2.pep
+    touch ${prefix}/${fasta}.TD2.bed
+    touch ${prefix}/${fasta}.TD2.cds
+    touch ${prefix}/${fasta}.TD2.gff3
+    touch ${prefix}/${fasta}.TD2.pep
     """
 }

From 734ba50ee560ed0a3cb45ae7d664ee0e51d61bdf Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Mon, 8 Dec 2025 18:19:30 +0100
Subject: [PATCH 10/18] Update meta.yml

---
 modules/nf-core/td2/longorfs/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/longorfs/meta.yml b/modules/nf-core/td2/longorfs/meta.yml
index 21607838e7ee..eab1d01c4515 100644
--- a/modules/nf-core/td2/longorfs/meta.yml
+++ b/modules/nf-core/td2/longorfs/meta.yml
@@ -58,7 +58,7 @@ topics:
       - TD2.LongOrfs:
           type: string
           description: The tool name
-      - "echo ${VERSION}":
+      - "${VERSION}":
           type: string
           description: The version of TD2 used
 authors:

From 248e24c0ab84584414033f3ca060b580e0b532f2 Mon Sep 17 00:00:00 2001
From: khersameesh24 <khersameesh24@gmail.com>
Date: Tue, 9 Dec 2025 00:29:47 +0100
Subject: [PATCH 11/18] resolving comments

---
 modules/nf-core/td2/longorfs/meta.yml         |   8 +-
 .../nf-core/td2/longorfs/tests/main.nf.test   |   4 +-
 .../td2/longorfs/tests/main.nf.test.snap      | 100 ++++--------------
 modules/nf-core/td2/predict/main.nf           |   2 +-
 modules/nf-core/td2/predict/meta.yml          |  10 +-
 .../td2/predict/tests/main.nf.test.snap       |  32 +++---
 6 files changed, 50 insertions(+), 106 deletions(-)

diff --git a/modules/nf-core/td2/longorfs/meta.yml b/modules/nf-core/td2/longorfs/meta.yml
index eab1d01c4515..a60281fac0aa 100644
--- a/modules/nf-core/td2/longorfs/meta.yml
+++ b/modules/nf-core/td2/longorfs/meta.yml
@@ -47,9 +47,9 @@ output:
       - TD2.LongOrfs:
           type: string
           description: The tool name
-      - "echo ${VERSION}":
+      - echo ${VERSION}:
           type: string
-          description: The version of TD2 used
+          description: The tool version
 topics:
   versions:
     - - ${task.process}:
@@ -58,9 +58,9 @@ topics:
       - TD2.LongOrfs:
           type: string
           description: The tool name
-      - "${VERSION}":
+      - echo ${VERSION}:
           type: string
-          description: The version of TD2 used
+          description: The tool version
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/modules/nf-core/td2/longorfs/tests/main.nf.test b/modules/nf-core/td2/longorfs/tests/main.nf.test
index 9f76f25c345e..cb677922fe9f 100644
--- a/modules/nf-core/td2/longorfs/tests/main.nf.test
+++ b/modules/nf-core/td2/longorfs/tests/main.nf.test
@@ -26,7 +26,7 @@ nextflow_process {
             assert process.success
             assertAll(
                 { assert snapshot(
-                    process.out,
+                    process.out.orfs,
                     process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
@@ -53,7 +53,7 @@ nextflow_process {
             assert process.success
             assertAll(
                 { assert snapshot(
-                    process.out,
+                    process.out.orfs,
                     process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
diff --git a/modules/nf-core/td2/longorfs/tests/main.nf.test.snap b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
index aa8376128b76..84654b480d53 100644
--- a/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
+++ b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
@@ -1,52 +1,24 @@
 {
     "td2.longorfs - transcriptome.fasta": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test_td2_longorfs"
-                        },
-                        [
-                            "longest_orfs.cds:md5,4226fe196a4527f938e25061ffe7eaf6",
-                            "longest_orfs.gff3:md5,864ae9147b65d07eb9d79c0e42968e12",
-                            "longest_orfs.pep:md5,0151dac6998be924139a4f5a5a0c590b"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        "TD2_LONGORFS",
-                        "TD2.LongOrfs",
-                        "td2: v1.0.6"
-                    ]
-                ],
-                "orfs": [
-                    [
-                        {
-                            "id": "test_td2_longorfs"
-                        },
-                        [
-                            "longest_orfs.cds:md5,4226fe196a4527f938e25061ffe7eaf6",
-                            "longest_orfs.gff3:md5,864ae9147b65d07eb9d79c0e42968e12",
-                            "longest_orfs.pep:md5,0151dac6998be924139a4f5a5a0c590b"
-                        ]
-                    ]
-                ],
-                "versions_td2": [
+            [
+                [
+                    {
+                        "id": "test_td2_longorfs"
+                    },
                     [
-                        "TD2_LONGORFS",
-                        "TD2.LongOrfs",
-                        "td2: v1.0.6"
+                        "longest_orfs.cds:md5,4226fe196a4527f938e25061ffe7eaf6",
+                        "longest_orfs.gff3:md5,864ae9147b65d07eb9d79c0e42968e12",
+                        "longest_orfs.pep:md5,0151dac6998be924139a4f5a5a0c590b"
                     ]
                 ]
-            },
+            ],
             {
                 "versions_td2": [
                     [
                         "TD2_LONGORFS",
                         "TD2.LongOrfs",
-                        "td2: v1.0.6"
+                        "v1.0.6"
                     ]
                 ]
             }
@@ -55,56 +27,28 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-04T21:11:35.499924547"
+        "timestamp": "2025-12-08T22:55:17.67412706"
     },
     "td2.longorfs - transcriptome.fasta -stub": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test_td2_longorfs"
-                        },
-                        [
-                            "longest_orfs.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "longest_orfs.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "longest_orfs.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        "TD2_LONGORFS",
-                        "TD2.LongOrfs",
-                        "td2: v1.0.6"
-                    ]
-                ],
-                "orfs": [
-                    [
-                        {
-                            "id": "test_td2_longorfs"
-                        },
-                        [
-                            "longest_orfs.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "longest_orfs.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "longest_orfs.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
-                    ]
-                ],
-                "versions_td2": [
+            [
+                [
+                    {
+                        "id": "test_td2_longorfs"
+                    },
                     [
-                        "TD2_LONGORFS",
-                        "TD2.LongOrfs",
-                        "td2: v1.0.6"
+                        "longest_orfs.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "longest_orfs.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "longest_orfs.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ]
-            },
+            ],
             {
                 "versions_td2": [
                     [
                         "TD2_LONGORFS",
                         "TD2.LongOrfs",
-                        "td2: v1.0.6"
+                        "v1.0.6"
                     ]
                 ]
             }
@@ -113,6 +57,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-04T21:13:55.06359889"
+        "timestamp": "2025-12-08T22:57:07.433423015"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/td2/predict/main.nf b/modules/nf-core/td2/predict/main.nf
index b83fddb182f8..7ea49b185589 100644
--- a/modules/nf-core/td2/predict/main.nf
+++ b/modules/nf-core/td2/predict/main.nf
@@ -11,7 +11,7 @@ process TD2_PREDICT {
     tuple val(meta), path(fasta), path(orfs_dir, stageAs: 'orfs')
 
     output:
-    tuple val(meta), path("${prefix}/*.TD2.{bed,cds,gff3,pep}"), emit: predictions
+    tuple val(meta), path("${prefix}/*.TD2.{bed,cds,gff3,pep}")        , emit: predictions
     tuple val("${task.process}"), val('TD2.Predict'), eval("echo ${VERSION}"), emit: versions_td2, topic: versions
 
     when:
diff --git a/modules/nf-core/td2/predict/meta.yml b/modules/nf-core/td2/predict/meta.yml
index 43bdbb5f71c1..e862ebc7e820 100644
--- a/modules/nf-core/td2/predict/meta.yml
+++ b/modules/nf-core/td2/predict/meta.yml
@@ -25,7 +25,7 @@ input:
     - fasta:
         type: file
         description: Transcripts fasta file
-        pattern: "*.{fasta}"
+        pattern: "*.fasta"
         ontologies: []
     - orfs_dir:
         type: file
@@ -53,9 +53,9 @@ output:
       - TD2.Predict:
           type: string
           description: The tool name
-      - "echo td2: ${VERSION}":
+      - echo ${VERSION}:
           type: string
-          description: The version of TD2 used
+          description: The tool version
 topics:
   versions:
     - - ${task.process}:
@@ -64,9 +64,9 @@ topics:
       - TD2.Predict:
           type: string
           description: The tool name
-      - "echo td2: ${VERSION}":
+      - echo ${VERSION}:
           type: string
-          description: The version of TD2 used
+          description: The tool version
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/modules/nf-core/td2/predict/tests/main.nf.test.snap b/modules/nf-core/td2/predict/tests/main.nf.test.snap
index d366015e16a2..2ad06a8c2ca5 100644
--- a/modules/nf-core/td2/predict/tests/main.nf.test.snap
+++ b/modules/nf-core/td2/predict/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                     [
                         "TD2_PREDICT",
                         "TD2.Predict",
-                        "td2: v1.0.6"
+                        "v1.0.6"
                     ]
                 ],
                 "predictions": [
@@ -39,7 +39,7 @@
                     [
                         "TD2_PREDICT",
                         "TD2.Predict",
-                        "td2: v1.0.6"
+                        "v1.0.6"
                     ]
                 ]
             },
@@ -48,7 +48,7 @@
                     [
                         "TD2_PREDICT",
                         "TD2.Predict",
-                        "td2: v1.0.6"
+                        "v1.0.6"
                     ]
                 ]
             }
@@ -57,7 +57,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-04T21:17:11.987007488"
+        "timestamp": "2025-12-08T22:59:14.906163868"
     },
     "td2.predict - transcriptome.fasta - stub": {
         "content": [
@@ -68,10 +68,10 @@
                             "id": "test_td2_predict"
                         },
                         [
-                            "fakefile.TD2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "fakefile.TD2.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "fakefile.TD2.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "fakefile.TD2.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            "genome.fasta.TD2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.TD2.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.TD2.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.TD2.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
                         ]
                     ]
                 ],
@@ -79,7 +79,7 @@
                     [
                         "TD2_PREDICT",
                         "TD2.Predict",
-                        "td2: v1.0.6"
+                        "v1.0.6"
                     ]
                 ],
                 "predictions": [
@@ -88,10 +88,10 @@
                             "id": "test_td2_predict"
                         },
                         [
-                            "fakefile.TD2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "fakefile.TD2.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "fakefile.TD2.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "fakefile.TD2.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            "genome.fasta.TD2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.TD2.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.TD2.gff3:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.TD2.pep:md5,d41d8cd98f00b204e9800998ecf8427e"
                         ]
                     ]
                 ],
@@ -99,7 +99,7 @@
                     [
                         "TD2_PREDICT",
                         "TD2.Predict",
-                        "td2: v1.0.6"
+                        "v1.0.6"
                     ]
                 ]
             },
@@ -108,7 +108,7 @@
                     [
                         "TD2_PREDICT",
                         "TD2.Predict",
-                        "td2: v1.0.6"
+                        "v1.0.6"
                     ]
                 ]
             }
@@ -117,6 +117,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-04T21:19:34.49914593"
+        "timestamp": "2025-12-08T23:01:07.402304947"
     }
 }
\ No newline at end of file

From e930683ba1f3c8e6b14678517d18b8dc5fdd846d Mon Sep 17 00:00:00 2001
From: khersameesh24 <khersameesh24@gmail.com>
Date: Tue, 9 Dec 2025 00:40:20 +0100
Subject: [PATCH 12/18] updated emad ontologies

---
 modules/nf-core/td2/longorfs/meta.yml | 8 ++++++--
 modules/nf-core/td2/predict/meta.yml  | 8 ++++++--
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/td2/longorfs/meta.yml b/modules/nf-core/td2/longorfs/meta.yml
index a60281fac0aa..5c14180aab5d 100644
--- a/modules/nf-core/td2/longorfs/meta.yml
+++ b/modules/nf-core/td2/longorfs/meta.yml
@@ -26,7 +26,8 @@ input:
         type: file
         description: Fasta file containing the target transcript sequences
         pattern: "*.{fasta}"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
 output:
   orfs:
     - - meta:
@@ -39,7 +40,10 @@ output:
           description: Files containing the longest ORFs predicted from the input
             transcript sequences
           pattern: "${prefix}/longest_orfs.{cds,gff3,pep}"
-          ontologies: []
+          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:
     - - ${task.process}:
           type: string
diff --git a/modules/nf-core/td2/predict/meta.yml b/modules/nf-core/td2/predict/meta.yml
index e862ebc7e820..2bc7995573ae 100644
--- a/modules/nf-core/td2/predict/meta.yml
+++ b/modules/nf-core/td2/predict/meta.yml
@@ -26,7 +26,8 @@ input:
         type: file
         description: Transcripts fasta file
         pattern: "*.fasta"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
     - orfs_dir:
         type: file
         description: Directory containing the ORF prediction files generated by
@@ -45,7 +46,10 @@ output:
           description: Files containing the TD2 ORF predictions for the input
             transcript sequences
           pattern: "${prefix}/*.TD2.{bed,cds,gff3,pep}"
-          ontologies: []
+          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

From 1d83372c609fa8a51e7ae73c2e4f51be1485660f Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Tue, 9 Dec 2025 17:44:24 +0000
Subject: [PATCH 13/18] Update
 modules/nf-core/td2/predict/tests/main.nf.test.snap

---
 modules/nf-core/td2/predict/tests/main.nf.test.snap | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/predict/tests/main.nf.test.snap b/modules/nf-core/td2/predict/tests/main.nf.test.snap
index 2ad06a8c2ca5..b877e74a0d77 100644
--- a/modules/nf-core/td2/predict/tests/main.nf.test.snap
+++ b/modules/nf-core/td2/predict/tests/main.nf.test.snap
@@ -48,7 +48,7 @@
                     [
                         "TD2_PREDICT",
                         "TD2.Predict",
-                        "v1.0.6"
+                        "1.0.6"
                     ]
                 ]
             }

From 24b2356a3f6306abf38e7b3b2783b9afa3ef094d Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Tue, 9 Dec 2025 17:44:32 +0000
Subject: [PATCH 14/18] Update modules/nf-core/td2/predict/main.nf

---
 modules/nf-core/td2/predict/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/predict/main.nf b/modules/nf-core/td2/predict/main.nf
index 7ea49b185589..cefd23653e2f 100644
--- a/modules/nf-core/td2/predict/main.nf
+++ b/modules/nf-core/td2/predict/main.nf
@@ -19,7 +19,7 @@ process TD2_PREDICT {
 
     script:
     def args = task.ext.args ?: ''
-    VERSION = 'v1.0.6' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    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}"
 
     """

From cf0a931efb257c7aefbbd4cf3626b03759a8cb3d Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Tue, 9 Dec 2025 17:44:40 +0000
Subject: [PATCH 15/18] Update
 modules/nf-core/td2/longorfs/tests/main.nf.test.snap

---
 modules/nf-core/td2/longorfs/tests/main.nf.test.snap | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/longorfs/tests/main.nf.test.snap b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
index 84654b480d53..c598d4a22ff9 100644
--- a/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
+++ b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
@@ -48,7 +48,7 @@
                     [
                         "TD2_LONGORFS",
                         "TD2.LongOrfs",
-                        "v1.0.6"
+                        "1.0.6"
                     ]
                 ]
             }

From e65e57b845ff9a9b10d65495f92bbdffc43635dd Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Tue, 9 Dec 2025 17:44:49 +0000
Subject: [PATCH 16/18] Update modules/nf-core/td2/longorfs/main.nf

---
 modules/nf-core/td2/longorfs/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/longorfs/main.nf b/modules/nf-core/td2/longorfs/main.nf
index 3c61a865c37a..addfcd06c454 100644
--- a/modules/nf-core/td2/longorfs/main.nf
+++ b/modules/nf-core/td2/longorfs/main.nf
@@ -19,7 +19,7 @@ process TD2_LONGORFS {
 
     script:
     def args = task.ext.args ?: ''
-    VERSION = 'v1.0.6' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    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}"
 
     """

From d341c3a830887e7b7d8d5eccef225d7d4400a623 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Tue, 9 Dec 2025 17:45:02 +0000
Subject: [PATCH 17/18] Update
 modules/nf-core/td2/predict/tests/main.nf.test.snap

---
 modules/nf-core/td2/predict/tests/main.nf.test.snap | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/predict/tests/main.nf.test.snap b/modules/nf-core/td2/predict/tests/main.nf.test.snap
index b877e74a0d77..30f62d67d6dc 100644
--- a/modules/nf-core/td2/predict/tests/main.nf.test.snap
+++ b/modules/nf-core/td2/predict/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                     [
                         "TD2_PREDICT",
                         "TD2.Predict",
-                        "v1.0.6"
+                        "1.0.6"
                     ]
                 ],
                 "predictions": [

From 2b9b4498b652b9d346e4c3182058fa5dc2166c3b Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Tue, 9 Dec 2025 17:45:13 +0000
Subject: [PATCH 18/18] Update
 modules/nf-core/td2/longorfs/tests/main.nf.test.snap

---
 modules/nf-core/td2/longorfs/tests/main.nf.test.snap | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/td2/longorfs/tests/main.nf.test.snap b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
index c598d4a22ff9..fd4f752a19a8 100644
--- a/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
+++ b/modules/nf-core/td2/longorfs/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     [
                         "TD2_LONGORFS",
                         "TD2.LongOrfs",
-                        "v1.0.6"
+                        "1.0.6"
                     ]
                 ]
             }