ENSGENOMIO-12 Module for running TRF

modules/ensembl/features/trf/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - trf=4.10.0rc2

modules/ensembl/features/trf/main.nf

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+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+process FEATURES_TRF {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "quay.io/biocontainers/trf:4.10.0rc2--h7b50bb2_0"
+
+    input:
+        tuple val(meta), path(fasta)
+
+    output:
+        tuple val(meta), path("*.dat"), emit: dat
+        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0"), emit: versions_trf, topic: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: '2 7 7 80 10 100 500 -d'
+        """
+        trf '${fasta}' ${args} -h
+        """
+
+    stub:
+        """
+        cat > "${fasta.name}.dat" << 'EOF'
+        Sequence: ${fasta.name}
+        EOF
+        """
+}

modules/ensembl/features/trf/meta.yml

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+---
+name: "features_trf"
+description: Detect tandem repeats in FASTA sequences with Tandem Repeats Finder.
+keywords:
+  - fasta
+  - features
+  - repeats
+  - tandem repeats
+  - trf
+  - genomio
+tools:
+  - "trf":
+      description: "Tandem Repeats Finder detects and reports tandem repeats in DNA sequences."
+      homepage: "https://tandem.bu.edu/trf/trf.html"
+      documentation: "https://tandem.bu.edu/trf/trf.html"
+      tool_dev_url: "https://tandem.bu.edu/trf/trf.html"
+      licence: ["custom"]
+      identifier: "biotools:trf"
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: FASTA file containing DNA sequence(s)
+        pattern: "*.{fa,fasta,fna}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929" # FASTA
+output:
+  dat:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.dat":
+          type: file
+          description: TRF repeat annotations in DAT format
+          pattern: "*.dat"
+  versions_trf:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - trf:
+          type: string
+          description: The tool name
+      - trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0:
+          type: eval
+          description: The expression to obtain the TRF version
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - trf:
+          type: string
+          description: The tool name
+      - trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0:
+          type: eval
+          description: The expression to obtain the TRF version
+authors:
+  - "ensembl-dev@ebi.ac.uk"
+maintainers:
+  - "ensembl-dev@ebi.ac.uk"

modules/ensembl/features/trf/tests/main.nf.test

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+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+// nf-core modules test features/trf
+nextflow_process {
+
+    name "Test Process FEATURES_TRF"
+    script "../main.nf"
+    process "FEATURES_TRF"
+
+    tag "features"
+    tag "features/trf"
+
+    test("Stub: TRF") {
+        when {
+            options "-stub"
+
+            process {
+                """
+                input[0] = [[ id: 'test' ],file('dummy.fa')
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+            assert process.out.dat.size() == 1
+            assert process.out.dat[0][0] == [ id: 'test' ]
+            assert file(process.out.dat[0][1]).name == 'dummy.fa.dat'
+            assert file(process.out.dat[0][1]).size() > 0
+            assert process.out.versions_trf.size() == 1
+        }
+    }
+}

modules/ensembl/features/trf/tests/main.nf.test.snap

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+{
+    "Stub: TRF": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "dummy.fa.dat:md5,7afa5cc8da76212b28fe6a2c4db74917"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FEATURES_TRF",
+                        "trf",
+                        "4.10.0"
+                    ]
+                ],
+                "dat": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "dummy.fa.dat:md5,7afa5cc8da76212b28fe6a2c4db74917"
+                    ]
+                ],
+                "versions_trf": [
+                    [
+                        "FEATURES_TRF",
+                        "trf",
+                        "4.10.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-06-25T13:50:41.590756",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
+    }
+}