nf-core · GallVp · May 19, 2025 · May 16, 2025 · May 16, 2025 · May 19, 2025
diff --git a/modules/nf-core/falint/environment.yml b/modules/nf-core/falint/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fa-lint=1.0.0
diff --git a/modules/nf-core/falint/main.nf b/modules/nf-core/falint/main.nf
@@ -0,0 +1,60 @@
+process FALINT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fa-lint:1.0.0--he881be0_0':
+        'biocontainers/fa-lint:1.0.0--he881be0_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path('*.success.log')  , emit: success_log , optional: true
+    tuple val(meta), path('*.error.log')    , emit: error_log   , optional: true
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    """
+    fa-lint \\
+        -threads ${task.cpus} \\
+        $args \\
+        -fasta $fasta \\
+        > >(tee ${prefix}.success.log >&1) \\
+        2> >(tee ${prefix}.error.log >&2) \\
+        || echo "Errors from fa-lint printed to ${prefix}.error.log"
+
+    if [ \$(cat ${prefix}.error.log | wc -l) -gt 0 ]; then
+        echo "Validation failed..."
+
+        rm ${prefix}.success.log
+    else
+        echo "Validation successful..."
+
+        rm ${prefix}.error.log
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fa-lint: \$(fa-lint -version)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "Fasta is valid: $fasta" \\
+        > "${prefix}.success.log"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fa-lint: \$(fa-lint -version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/falint/meta.yml b/modules/nf-core/falint/meta.yml
@@ -0,0 +1,61 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "falint"
+description: A fasta linter/validator
+keywords:
+  - fasta
+  - validation
+  - genome
+tools:
+  - "falint":
+      description: "A Fasta linter/validator"
+      homepage: "https://github.com/GallVp/fa-lint"
+      documentation: "https://github.com/GallVp/fa-lint"
+      tool_dev_url: "https://github.com/GallVp/fa-lint"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing file information
+          e.g. [ id:'test' ]
+    - fasta:
+        type: file
+        description: Input fasta file
+        pattern: "*.fasta"
+        ontologies: []
+output:
+  - success_log:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing file information
+            e.g. [ id:'test' ]
+      - "*.success.log":
+          type: file
+          description: Log file for successful validation
+          pattern: "*.success.log"
+          ontologies: []
+  - error_log:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing file information
+            e.g. [ id:'test' ]
+      - "*.error.log":
+          type: file
+          description: Log file for failed validation
+          pattern: "*.error.log"
+          ontologies: []
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@gallvp"
+maintainers:
+  - "@gallvp"
diff --git a/modules/nf-core/falint/tests/main.nf.test b/modules/nf-core/falint/tests/main.nf.test
@@ -0,0 +1,80 @@
+nextflow_process {
+
+    name "Test Process FALINT"
+    script "../main.nf"
+    process "FALINT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "falint"
+
+    test("sarscov2-fasta-valid") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2-fasta-valid-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2-gff3-invalid") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert process.out.success_log == [] },
+                { assert file(process.out.error_log[0][1]).text.contains('Fasta file must start with a header line') }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/falint/tests/main.nf.test.snap b/modules/nf-core/falint/tests/main.nf.test.snap
@@ -0,0 +1,96 @@
+{
+    "sarscov2-fasta-valid": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.success.log:md5,7b9802635c4f44d1711e7132ccdb648e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+                ],
+                "error_log": [
+
+                ],
+                "success_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.success.log:md5,7b9802635c4f44d1711e7132ccdb648e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.6"
+        },
+        "timestamp": "2025-05-16T14:55:29.853456"
+    },
+    "sarscov2-gff3-invalid": {
+        "content": [
+            [
+                "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.6"
+        },
+        "timestamp": "2025-05-16T15:08:29.434346"
+    },
+    "sarscov2-fasta-valid-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.success.log:md5,7b9802635c4f44d1711e7132ccdb648e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+                ],
+                "error_log": [
+
+                ],
+                "success_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.success.log:md5,7b9802635c4f44d1711e7132ccdb648e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.6"
+        },
+        "timestamp": "2025-05-16T15:08:25.052305"
+    }
+}