Added gt/stat (#5577)

* Added gt/stat

* Fixed typo in pattern

modules/nf-core/gt/stat/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "gt_stat"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::genometools-genometools=1.6.5"

modules/nf-core/gt/stat/main.nf

@@ -0,0 +1,46 @@
+process GT_STAT {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/genometools-genometools:1.6.5--py310h3db02ab_0':
+        'biocontainers/genometools-genometools:1.6.5--py310h3db02ab_0' }"
+
+    input:
+    tuple val(meta), path(gff3)
+
+    output:
+    tuple val(meta), path("${prefix}.yml")  , emit: stats
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args    = task.ext.args ?: ''
+    prefix      = task.ext.prefix ?: "${meta.id}"
+    """
+    gt \\
+        stat \\
+        $args \\
+        $gff3 \\
+        > ${prefix}.yml
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genometools: \$(gt --version | head -1 | sed 's/gt (GenomeTools) //')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix      = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.yml
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genometools: \$(gt --version | head -1 | sed 's/gt (GenomeTools) //')
+    END_VERSIONS
+    """
+}

modules/nf-core/gt/stat/meta.yml

@@ -0,0 +1,46 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "gt_stat"
+description: "GenomeTools gt-stat utility to show statistics about features contained in GFF3 files"
+keywords:
+  - genome
+  - gff3
+  - annotation
+  - statistics
+  - stats
+tools:
+  - "gt":
+      description: "The GenomeTools genome analysis system"
+      homepage: "https://genometools.org/index.html"
+      documentation: "https://genometools.org/documentation.html"
+      tool_dev_url: "https://github.com/genometools/genometools"
+      doi: "10.1109/TCBB.2013.68"
+      licence: ["ISC"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test' ]`
+  - gff3:
+      type: file
+      description: Input gff3 file
+      pattern: "*.{gff,gff3}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test' ]`
+  - stats:
+      type: file
+      description: Stats file in yaml format
+      pattern: "*.yml"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@GallVp"
+maintainers:
+  - "@GallVp"

modules/nf-core/gt/stat/tests/main.nf.test

@@ -0,0 +1,62 @@
+nextflow_process {
+
+    name "Test Process GT_STAT"
+    script "../main.nf"
+    process "GT_STAT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gt"
+    tag "gt/stat"
+
+    test("sarscov2-gff3") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    "##gff-version 3" +
+                    file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true).text.toLowerCase()
+                )
+                .collectFile(name: 'sample.gff3', newLine: true)
+                .map { file -> [ [ id:'test' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(process.out.stats[0][1]).text.contains("cdss: 12") }
+            )
+        }
+
+    }
+
+    test("sarscov2-gff3-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.stats != null }, // md5sum for empty files not allowed by nf-core/tools 2.14.0
+                { assert snapshot(process.out.versions).match("stub_versions") }
+            )
+        }
+
+    }
+
+}

modules/nf-core/gt/stat/tests/main.nf.test.snap

@@ -0,0 +1,47 @@
+{
+    "sarscov2-gff3": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.yml:md5,ebba7831ddbf916b8bbea675ba8693b5"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a184b50afb2ad6dd2d3d37b0a211dd71"
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.yml:md5,ebba7831ddbf916b8bbea675ba8693b5"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a184b50afb2ad6dd2d3d37b0a211dd71"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-09T19:29:08.925383"
+    },
+    "stub_versions": {
+        "content": [
+            [
+                "versions.yml:md5,a184b50afb2ad6dd2d3d37b0a211dd71"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-09T19:29:12.808817"
+    }
+}

modules/nf-core/gt/stat/tests/tags.yml

@@ -0,0 +1,2 @@
+gt/stat:
+  - "modules/nf-core/gt/stat/**"