Add ciri2 module

modules/nf-core/ciri2/environment.yml

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+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::ciri2=2.0.6=pl5321hdfd78af_0"

modules/nf-core/ciri2/main.nf

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+
+process CIRI2 {
+    tag "$meta.id"
+    label 'process_single'
+
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ciri2:2.0.6--pl5321hdfd78af_0':
+        'quay.io/biocontainers/ciri2:2.0.6--pl5321hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(sam) // Required input sam_file
+    path  fasta     // optional reference fasta file
+    path  annotation        // optional GTF or GFF3 annotation file
+    path  ref_dir      // optional reference directory path
+
+    output:
+
+    tuple val(meta), path("*.txt"), emit: circrna
+    tuple val(meta), path("*.txt.log"), emit: log, optional: true
+    tuple val(meta), path("CIRIerror.log"), emit: error_log, optional: true
+
+    tuple val("${task.process}"), val('CIRI2.pl'), eval("CIRI2.pl --help | sed -n 's/^Version:\\s*//p'"), topic: versions, emit: versions_ciri2
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def anno = annotation ? "--anno ${annotation}" : ""
+    def reference = fasta ? "--ref_file ${fasta}" : "--ref_dir ${ref_dir}"
+
+    """
+    CIRI2.pl \\
+        --in $sam \\
+        --out ${prefix}.txt \\
+        $reference \\
+        $anno \\
+        --thread_num $task.cpus \\
+        $args
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo $args
+
+    touch ${prefix}.txt
+    """
+}

modules/nf-core/ciri2/meta.yml

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+name: "ciri2"
+description: Circular RNA identification based on multiple seed matching
+keywords:
+  - circRNA
+  - detection
+  - genomics
+  - transcriptomics
+tools:
+  - "ciri2":
+      description: "CIRI2: Circular RNA identification based on multiple seed matching"
+      homepage: "https://ciri-cookbook.readthedocs.io/en/latest/CIRI2.html"
+      documentation: "https://ciri-cookbook.readthedocs.io/en/latest/CIRI2.html"
+      tool_dev_url: "https://github.com/bioinfo-biols/CIRI-full/tree/master/bin/CIRI_v2.0.6"
+      doi: "10.1093/bib/bbx014"
+      licence:
+        - "GPL-2.0-only"
+      identifier: "biotools:ciri2"
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - sam:
+        type: file
+        description: Raw SAM file from BWA
+        pattern: "*.{sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3462"
+  - fasta:
+      type: file
+      description: Fasta file for reference sequence
+      pattern: "*.{fasta, fa}"
+      ontologies:
+        - edam: "http://edamontology.org/format_1929"
+  - annotation:
+      type: file
+      description: GTF or GFF3 annotation file
+      pattern: "*.{gtf, gff, gff3}"
+      ontologies:
+        - edam: "http://edamontology.org/format_2305"
+  - ref_dir:
+      type: directory
+      description: Directory containing reference files
+output:
+  circrna:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.txt":
+          type: file
+          description: Output file containing circRNA list
+          pattern: "*.{txt}"
+          ontologies: []
+  log:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.txt.log":
+          type: file
+          description: Output log file
+          pattern: "*.{txt.log}"
+          ontologies: []
+  error_log:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - CIRIerror.log:
+          type: file
+          description: Output error log file
+          pattern: "CIRIerror.log"
+          ontologies: []
+  versions_ciri2:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - CIRI2.pl:
+          type: string
+          description: The name of the tool
+      - CIRI2.pl --help | sed -n 's/^Version:\s*//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - CIRI2.pl:
+          type: string
+          description: The name of the tool
+      - CIRI2.pl --help | sed -n 's/^Version:\s*//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@razmia02"
+maintainers:
+  - "@razmia02"

modules/nf-core/ciri2/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process CIRI2"
+    script "../main.nf"
+    process "CIRI2"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ciri2"
+    tag "samtools/view"
+
+    setup {
+        run("SAMTOOLS_VIEW") {
+            script "../../samtools/view/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end: false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.bam', checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                    [ id:'fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), [] ]
+                input[2] = [ [], [] ]
+                input[3] = [ [], [] ]
+                input[4] = []
+                """
+            }
+        }
+    }
+
+    test("homo_sapiens - sam - pairedend") {
+
+        when {
+            process {
+                """
+                input[0] = SAMTOOLS_VIEW.out.sam
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.circrna[0][1]).name,
+                    process.out.logfile ? file(process.out.logfile[0][1]).name : null,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - sam - pairedend -- stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end: false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.bam', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.circrna,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+    }
+}

modules/nf-core/ciri2/tests/main.nf.test.snap

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+{
+    "homo_sapiens - sam - pairedend": {
+        "content": [
+            "test.txt",
+            null,
+            {
+                "versions_ciri2": [
+                    [
+                        "CIRI2",
+                        "CIRI2.pl",
+                        "2.0.6"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-24T19:44:07.04302318",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
+    },
+    "homo_sapiens - sam - pairedend -- stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            {
+                "versions_ciri2": [
+                    [
+                        "CIRI2",
+                        "CIRI2.pl",
+                        "2.0.6"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-24T19:44:21.142901021",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
+    }
+}

modules/nf-core/ciri2/tests/nextflow.config

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+process {
+    withName: 'SAMTOOLS_VIEW' {
+        ext.args = '--output-fmt sam'
+    }
+}