proovframe map init push (#6790)

* proovframe map init push

* stub test renamed properly

* text contains test instead, because conda was failing (produces 0s column isntead of a values column)

* meta spacing fixed

modules/nf-core/proovframe/map/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::proovframe=0.9.7"

modules/nf-core/proovframe/map/main.nf

@@ -0,0 +1,48 @@
+process PROOVFRAME_MAP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/proovframe:0.9.7--hdfd78af_1':
+        'biocontainers/proovframe:0.9.7--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(faa), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    proovframe \\
+        map \\
+        ${args} \\
+        -a ${faa} \\
+        -o ${prefix}.tsv  \\
+        ${fasta}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        proovframe: 0.9.7
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        proovframe: 0.9.7
+    END_VERSIONS
+    """
+}

modules/nf-core/proovframe/map/meta.yml

@@ -0,0 +1,56 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "proovframe_map"
+description: frame-shift correction for long read (meta)genomics - maps proteins to reads
+keywords:
+  - frame-shift correction
+  - long-read sequencing
+  - sequence analysis
+tools:
+  - "proovframe":
+      description: "frame-shift correction for long read (meta)genomics"
+      homepage: "https://github.com/thackl/proovframe"
+      documentation: "https://github.com/thackl/proovframe"
+      tool_dev_url: "https://github.com/thackl/proovframe"
+      doi: "10.1101/2021.08.23.457338"
+      licence: ["MIT"]
+      identifier: biotools:proovframe
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - faa:
+        type: file
+        description: A FASTA file containing a database of guide protein sequences
+        pattern: "*.{faa,fasta,fa}"
+    - fasta:
+        type: file
+        description: A FASTA file containing raw read nucleotide sequences
+        pattern: "*.{fasta,fa}"
+
+output:
+  - tsv:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.tsv":
+          type: file
+          description: Output TSV file with the frameshift-aware protein to read alignments
+          pattern: "*.tsv"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@manuelcarbajo"
+  - "@MGS-sails"
+  - "@vagkaratzas"
+maintainers:
+  - "@vagkaratzas"

modules/nf-core/proovframe/map/tests/main.nf.test

@@ -0,0 +1,59 @@
+nextflow_process {
+
+    name "Test Process PROOVFRAME_MAP"
+    script "../main.nf"
+    process "PROOVFRAME_MAP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "proovframe"
+    tag "proovframe/map"
+
+    test("sarscov2 - tsv") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.tsv[0][1]).text.contains('MT192765.1	ENSSASP00005000002.1	100.0	7096	1	0	259	21545	1') },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - tsv - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/proovframe/map/tests/main.nf.test.snap

@@ -0,0 +1,49 @@
+{
+    "sarscov2 - tsv": {
+        "content": [
+            [
+                "versions.yml:md5,f49f29b8134fdb539364ee46855eb313"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
+        },
+        "timestamp": "2024-10-16T15:02:00.599243234"
+    },
+    "sarscov2 - tsv - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f49f29b8134fdb539364ee46855eb313"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f49f29b8134fdb539364ee46855eb313"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
+        },
+        "timestamp": "2024-10-16T15:02:21.855444606"
+    }
+}