added cmscan process used in rfam pipeline

modules/ensembl/infernal/cmscan/environment.yml

@@ -0,0 +1,6 @@
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::infernal=1.1.5

modules/ensembl/infernal/cmscan/main.nf

@@ -0,0 +1,74 @@
+// 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.enable.types = true
+
+process CMSCAN {
+    tag "${meta.id}"
+    label 'process_high'
+
+    conda "bioconda::infernal=1.1.5"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/infernal:1.1.5--pl5321h7b50bb2_4' :
+        'quay.io/biocontainers/infernal:1.1.5--pl5321h7b50bb2_4' }"
+
+    input:
+        record(
+            meta:  Map,
+            chunk: Path,
+            rfam_filtered_cm: Path
+        )
+
+    output:
+        record(
+            meta:   meta,
+            tblout: file("*.tblout")
+        )
+
+    topic:
+        tuple(
+            task.process,
+            'infernal',
+            eval("cmscan -h 2>&1 | sed -nE 's/^# INFERNAL ([^ ]+).*/\\1/p'")
+        ) >> 'versions'
+
+    script:
+        def prefix = task.ext.prefix
+            ? "${task.ext.prefix}.${meta.id}.${task.index}"
+            : "${meta.id}.${task.index}"
+        """
+        cmpress ${rfam_filtered_cm}
+        cmscan --rfam --nohmmonly --cut_ga \\
+        --notextw \\
+        --fmt 2 \\
+        --cpu ${task.cpus} \\
+        --tblout ${prefix}.tblout \\
+        ${rfam_filtered_cm} \\
+        ${chunk}
+
+        """
+
+    stub:
+        def prefix = task.ext.prefix
+            ? "${task.ext.prefix}.${meta.id}.${task.index}"
+            : "${meta.id}.${task.index}"
+        """
+        touch ${prefix}.tblout
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            infernal: "stub"
+        END_VERSIONS
+        """
+}

modules/ensembl/infernal/cmscan/meta.yml

@@ -0,0 +1,40 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: CMSCAN
+description: Search genome FASTA chunks against an Rfam covariance model database with Infernal cmscan.
+keywords:
+  - infernal
+  - cmscan
+  - rfam
+  - covariance model
+tools:
+  - infernal:
+      description: Infernal RNA homology search and alignment tools.
+      homepage: http://eddylab.org/infernal/
+      documentation: http://eddylab.org/infernal/
+      licence: ["BSD-3-Clause"]
+input:
+  - - meta:
+        type: map
+        description: Groovy Map containing sample information, including a unique id.
+    - chunk:
+        type: file
+        description: FASTA chunk to scan.
+        pattern: "*.{fa,fasta,fna}"
+    - rfam_filtered_cm:
+        type: file
+        description: Rfam covariance model database used for scanning.
+        pattern: "*.cm{,.gz}"
+output:
+  tblout:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information.
+      - "*.tblout":
+          type: file
+          description: Tabular cmscan hits for the input chunk.
+          pattern: "*.tblout"
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions.
+        pattern: "versions.yml"

modules/ensembl/infernal/cmscan/tests/main.nf.test

@@ -0,0 +1,72 @@
+// 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 CMSCAN"
+    script "../main.nf"
+    process "CMSCAN"
+
+    tag "modules"
+    tag "modules_local"
+    tag "infernal"
+    tag "cmscan"
+
+    test("should produce a cmscan tblout file") {
+
+        options "-stub-run"
+
+        when {
+            process {
+                """
+                chunk_file = Channel.of(
+                    '>test',
+                    'ACGTACGTACGT'
+                )
+                .collectFile(name: 'test_chunk.fa', newLine: true)
+
+                rfam_cm_file = Channel.of(
+                    'INFERNAL 1.1',
+                    'NAME test_model',
+                    'ACC RF00001',
+                    'GA 10.0',
+                    '//'
+                )
+                .collectFile(name: 'rfam_filtered.cm', newLine: true)
+
+                input[0] = chunk_file
+                    .combine(rfam_cm_file)
+                    .map { chunk, rfam_cm ->
+                        record(
+                            meta: [id: 'test'],
+                            chunk: chunk,
+                            rfam_filtered_cm: rfam_cm
+                        )
+                    }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.size() == 1 },
+                { assert process.out[0][0].meta.id == 'test' },
+                { assert path(process.out[0][0].tblout instanceof List ? process.out[0][0].tblout[0] : process.out[0][0].tblout).fileName.toString().endsWith('.tblout') },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/ensembl/infernal/cmscan/tests/main.nf.test.snap

@@ -0,0 +1,21 @@
+{
+    "should produce a cmscan tblout file": {
+        "content": [
+            {
+                "0": [
+                    {
+                        "meta": {
+                            "id": "test"
+                        },
+                        "tblout": "test.1.tblout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    }
+                ]
+            }
+        ],
+        "timestamp": "2026-09-25T18:22:53.008883237",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    }
+}