new module: yte

modules/nf-core/yte/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::yte=1.9.0

modules/nf-core/yte/main.nf

@@ -0,0 +1,53 @@
+process YTE {
+    tag "$meta.id"
+    label 'process_single'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    conda "${moduleDir}/environment.yml"
+
+    // TODO: update container to 1.9.0
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/yte:1.5.4--2466971526dcd2a8':
+        'community.wave.seqera.io/library/yte:1.5.4--36d16ca4bab836c1' }"
+
+    input:
+    tuple val(meta), path(template)
+    path(map_file)
+    val(map)
+
+    output:
+    tuple val(meta), path("*.yaml"), emit: rendered
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    // Use map_file if provided, otherwise use map to create key=value pairs for mapping command
+    def mapping_cmd = map_file ? "--variable-file ${map_file}" : "--variables " + map.collect { k, v -> "${k}=${v}" }.join(' ')
+    VERSION = "1.5.4" // WARN: Version information not provided by tool on CLI. Please update this string when bumping
+    """
+    yte ${mapping_cmd} < ${template} > ${prefix}.yaml
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        yte: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    VERSION = "1.5.4" // WARN: Version information not provided by tool on CLI. Please update this string when bumping
+    """
+    touch ${prefix}.yaml
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        yte: $VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/yte/meta.yml

@@ -0,0 +1,62 @@
+name: yte
+description: A YAML template engine with Python expressions
+keywords:
+  - yaml
+  - template
+  - python
+tools:
+  - yte:
+      description: "A YAML template engine with Python expressions"
+      homepage: "https://yte-template-engine.github.io/"
+      documentation: "https://yte-template-engine.github.io/"
+      tool_dev_url: "https://github.com/yte-template-engine/yte"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'template1' ]`
+    - template:
+        type: file
+        description: YTE template
+        pattern: "*.{yaml}"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+  - - map_file:
+        type: file
+        description: YAML file containing a map to be used in the template
+        pattern: "*.{yaml}"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+  - - map:
+        type: map
+        description: |
+          Groovy Map containing mapping information to be used in the template
+          e.g. `[ key: value ]` with key being a wildcard in the template
+
+output:
+  - rendered:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.yaml":
+          type: file
+          description: Rendered YAML file
+          pattern: "*.yaml"
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # YAML
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # YAML
+
+authors:
+  - "@famosab"
+maintainers:
+  - "@famosab"

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

@@ -0,0 +1,111 @@
+nextflow_process {
+
+    name "Test Process YTE"
+    script "../main.nf"
+    process "YTE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "yte"
+
+    test("yaml - map") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'template' ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/1d7285ed7dea21f2d4079f7daa196b9f17bc6e85/data/generic/config/config_template.yte.yaml', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = [ 'sex': 'female' ] // map
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("yaml - map - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'template' ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/1d7285ed7dea21f2d4079f7daa196b9f17bc6e85/data/generic/config/config_template.yte.yaml', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = [ 'sex': 'female' ] // map
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("yaml - map_file") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'template' ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/1d7285ed7dea21f2d4079f7daa196b9f17bc6e85/data/generic/config/config_template.yte.yaml', checkIfExists: true)
+                ]
+                input[1] = [file ('https://raw.githubusercontent.com/nf-core/test-datasets/811dd3fa80dbac64b14f07413ad78bb2bebe0323/data/generic/config/yte_map_file.yaml', checkIfExists: true)]
+                input[2] = [] // map
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("yaml - map_file - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'template' ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/1d7285ed7dea21f2d4079f7daa196b9f17bc6e85/data/generic/config/config_template.yte.yaml', checkIfExists: true)
+                ]
+                input[1] = [file ('https://raw.githubusercontent.com/nf-core/test-datasets/811dd3fa80dbac64b14f07413ad78bb2bebe0323/data/generic/config/yte_map_file.yaml', checkIfExists: true)]
+                input[2] = [] // map
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,68 @@
+{
+    "yaml - no_template": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "no_template"
+                        },
+                        "no_template.yaml:md5,a22cd4fd5af79c7c1f17f5decbfc1a8e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,efd610134e8fc0892fddb2c50121e097"
+                ],
+                "rendered": [
+                    [
+                        {
+                            "id": "no_template"
+                        },
+                        "no_template.yaml:md5,a22cd4fd5af79c7c1f17f5decbfc1a8e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,efd610134e8fc0892fddb2c50121e097"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-26T15:39:14.259911"
+    },
+    "yaml - no_template - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "no_template"
+                        },
+                        "no_template.yaml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,efd610134e8fc0892fddb2c50121e097"
+                ],
+                "rendered": [
+                    [
+                        {
+                            "id": "no_template"
+                        },
+                        "no_template.yaml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,efd610134e8fc0892fddb2c50121e097"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-26T15:39:18.386795"
+    }
+}