Add ciri2 module

modules/nf-core/ciri2/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::ciri2=2.0.6"

modules/nf-core/ciri2/main.nf

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+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+process CIRI2 {
+    tag "$meta.id"
+    label 'process_single'
+
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ciri2:2.0.6--pl5321hdfd78af_0':
+        'quay.io/biocontainers/ciri2:2.0.6--pl5321hdfd78af_0' }"
+
+    input:// TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               This information may not be required in some instances e.g. indexing reference genome files:
+    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
+    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
+    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
+    tuple val(meta), path(sam) // Required -I sam_file
+    path  fasta     // optional -F reference fasta file
+    path  annotation        // optional -A GTF or GFF3 annotation file
+    path  ref_dir      // optional -R reference directory path
+
+    output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    tuple val(meta), path("*.txt"), emit: circrna
+    tuple val(meta), path("*.log"), emit: logfile, optional: true
+
+    // TODO nf-core: Update the command here to obtain the version number of the software used in this module
+    // TODO nf-core: If multiple software packages are used in this module, all MUST be added here
+    //               by copying the line below and replacing the current tool with the extra tool(s)
+    tuple val("${task.process}"), val('ciri2'), eval("ciri2 --version"), 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 ? "-A ${annotation}" : ""
+    def reference = fasta ? "-F ${fasta}" : "-R ${ref_dir}"
+    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
+    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
+    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    // TODO nf-core: Please replace the example samtools command below with your module's command
+    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    """
+    perl CIRI2.pl \\
+        -I $sam \\
+        -O ${prefix}.txt \\
+        $reference \\
+        $anno \\
+        -T $task.cpus \\
+        $args
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
+    //               Have a look at the following examples:
+    //               Simple example: https://github.com/nf-core/modules/blob/624977dfaf562211e68a8a868ca80acc8461f1ac/modules/nf-core/cutadapt/main.nf#L34-L46
+    //               Complex example: https://github.com/nf-core/modules/blob/88d43dad73a675e66bff49ebb57fe657a5909018/modules/nf-core/bedtools/split/main.nf#L32-L43
+    // TODO nf-core: If the module doesn't use arguments ($args), you SHOULD remove:
+    //               - The definition of args `def args = task.ext.args ?: ''` above.
+    //               - The use of the variable in the script `echo $args ` below.
+    """
+    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: []
+  versions_ciri2:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - ciri2:
+          type: string
+          description: The name of the tool
+      - ciri2 --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+  logfile:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.log":
+          type: file
+          description: Output logfile
+          pattern: "*.{log}"
+          ontologies: []
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - ciri2:
+          type: string
+          description: The name of the tool
+      - ciri2 --version:
+          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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+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test ciri2
+nextflow_process {
+
+    name "Test Process CIRI2"
+    script "../main.nf"
+    process "CIRI2"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ciri2"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the nf-test docs (https://www.nf-test.com/docs/testcases/setup/).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/developing/testing/assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}