Module for running Red repeat detector

modules/ensembl/features/red/environment.yml

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+---
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - red=2018.09.10

modules/ensembl/features/red/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_RED {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "quay.io/biocontainers/red:2018.09.10--h9948957_3"
+
+    input:
+        tuple val(meta), path(fasta)
+
+    output:
+        tuple val(meta), path("rpt/*.bed"), emit: bed
+        tuple val("${task.process}"), val('red'), eval("conda list red --json | python -c 'import sys,json; print(json.load(sys.stdin)[0][\"version\"])' || echo 2.0"), emit: versions_red, topic: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+
+        def reserved = ['-gnm', '-rpt', '-msk', '-frm', '-cor']
+        def supplied = args.tokenize()
+
+        supplied.each { opt ->
+            if (opt in reserved) {
+                error "FEATURES_RED: ${opt} is managed by the module and must not be supplied via task.ext.args."
+            }
+        }
+
+        """
+        mkdir -p genome rpt
+
+        # Red only processes .fa files in the genome directory
+        ln -snf \$(realpath "${fasta}") genome/${meta.id}.fa
+
+        Red \
+            -gnm genome \
+            -rpt rpt \
+            -cor ${task.cpus} \
+            -frm 2 \
+            ${args}
+        """
+
+    stub:
+        """
+        mkdir -p rpt
+
+        cat > rpt/${meta.id}.bed <<EOF
+        ${meta.id}\t1\t100
+        EOF
+        """
+}

modules/ensembl/features/red/meta.yml

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+---
+name: "features_red"
+description: Detect repeats de novo in genome FASTA sequences with Red.
+keywords:
+  - fasta
+  - features
+  - repeats
+  - de novo repeats
+  - red
+  - genomio
+tools:
+  - "red":
+      description: "Red detects repeats de novo on the genomic scale."
+      homepage: "http://toolsmith.ens.utulsa.edu"
+      documentation: "http://toolsmith.ens.utulsa.edu"
+      tool_dev_url: "http://toolsmith.ens.utulsa.edu"
+      doi: "10.1186/s12859-015-0654-5"
+      licence: ["custom"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: FASTA file containing genome sequence(s).
+        pattern: "*.{fa,fasta,fna}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929" # FASTA
+output:
+  rpt:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "rpt/*.bed":
+          type: file
+          description: Red repeat report file.
+          pattern: "*.bed"
+  versions_red:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - red:
+          type: string
+          description: The tool name
+      - conda list red --json | python -c 'import sys,json; print(json.load(sys.stdin)[0]["version"])' || echo 2.0:
+          type: eval
+          description: The expression to obtain the Red version
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - red:
+          type: string
+          description: The tool name
+      - conda list red --json | python -c 'import sys,json; print(json.load(sys.stdin)[0]["version"])' || echo 2.0:
+          type: eval
+          description: The expression to obtain the Red version
+authors:
+  - "ensembl-dev@ebi.ac.uk"
+maintainers:
+  - "ensembl-dev@ebi.ac.uk"

modules/ensembl/features/red/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.
+
+nextflow_process {
+
+    name "Test Process FEATURES_RED"
+    script "../main.nf"
+    process "FEATURES_RED"
+
+    tag "modules"
+    tag "modules_local"
+    tag "features"
+    tag "features/red"
+
+    test("Stub creates Red repeat report") {
+
+        when {
+            options "-stub"
+
+            process {
+                """
+                def fasta = file("test.fa")
+                fasta.text = ">test\\nACGT\\n"
+
+                input[0] = [[ id:'test' ], fasta]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+            assert process.out.bed.size() == 1
+            assert process.out.bed[0][0] == [ id: 'test' ]
+            assert file(process.out.bed[0][1]).name == "test.bed"
+            assert file(process.out.bed[0][1]).size() > 0
+            assert process.out.versions_red.size() == 1
+        }
+    }
+}

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

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+{
+    "Stub creates Red repeat report": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,aa604b48150afc506072a1f9656b6bb7"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FEATURES_RED",
+                        "red",
+                        "2.0"
+                    ]
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,aa604b48150afc506072a1f9656b6bb7"
+                    ]
+                ],
+                "versions_red": [
+                    [
+                        "FEATURES_RED",
+                        "red",
+                        "2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-14T16:03:16.866216",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
+    }
+}