Add mifaser

modules/nf-core/mifaser/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::mifaser=1.60

modules/nf-core/mifaser/main.nf

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+process MIFASER {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container 'ghcr.io/vdblab/mifaser:1.64d'
+
+    input:
+    tuple val(meta), path(reads)
+    path db
+
+    output:
+    tuple val(meta), path("*multi_ec.tsv"), emit: multi_ec
+    tuple val(meta), path("*analysis.tsv"), emit: analysis
+    tuple val(meta), path("*ec_count.tsv"), emit: ec_counts
+    tuple val("${task.process}"), val('mi-faser'), eval("mifaser --version 2>&1 | sed 's/* v//'"), emit: versions_mifaser, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args       = task.ext.args   ?: ''
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    def input_flag = meta.single_end  ? "-f" : "-l"
+    """
+    mifaser \\
+        ${args} \\
+        ${input_flag} ${reads} \\
+        --threads 1 \\
+        --cpu ${task.cpus} \\
+        --databasefolder ${db} \\
+        --outputfolder mifaser-${prefix}/
+
+    for suf in multi_ec.tsv analysis.tsv ec_count.tsv; do
+        mv mifaser-${prefix}/\${suf} ${prefix}_\${suf}
+    done
+    """
+
+    stub:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+    for suf in multi_ec.tsv analysis.tsv ec_count.tsv; do
+        touch ${prefix}_\${suf}
+    done
+    """
+}

modules/nf-core/mifaser/meta.yml

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+name: "mifaser"
+description: Functional annotation of metagenomic reads by assigning enzyme
+  commission (EC) numbers
+keywords:
+  - metagenomics
+  - functional annotation
+  - EC numbers
+  - fastq
+tools:
+  - "mifaser":
+      description: "mi-faser: microsecond functional annotation of sequences, a massive
+        scalability upgrade"
+      homepage: "https://sourceforge.net/projects/mifaser/"
+      documentation: "https://sourceforge.net/projects/mifaser/"
+      tool_dev_url: "https://sourceforge.net/projects/mifaser/"
+      doi: "10.1093/nar/gkx1209"
+      licence:
+        - "NPOSL-3.0"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:true ]`
+    - reads:
+        type: file
+        description: |
+          Single-end or paired-end FASTQ files. Use meta.single_end to indicate input type.
+        pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1930"
+  - db:
+      type: directory
+      description: Path to the mi-faser database folder
+output:
+  multi_ec:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*multi_ec.tsv":
+          type: file
+          description: TSV file with multi-EC functional assignments per read
+          pattern: "*multi_ec.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475
+  analysis:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*analysis.tsv":
+          type: file
+          description: TSV file with per-sample functional analysis summary
+          pattern: "*analysis.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475
+  ec_counts:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*ec_count.tsv":
+          type: file
+          description: TSV file with EC number counts
+          pattern: "*ec_count.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475
+  versions_mifaser:
+    - - "${task.process}":
+          type: string
+          description: Process name
+      - "mi-faser":
+          type: string
+          description: Tool name
+      - "mifaser --version 2>&1 | sed 's/* v//'":
+          type: eval
+          description: mifaser version string
+topics:
+  versions:
+    - - "${task.process}":
+          type: string
+          description: Process name
+      - "mi-faser":
+          type: string
+          description: Tool name
+      - "mifaser --version 2>&1 | sed 's/* v//'":
+          type: eval
+          description: mifaser version string
+authors:
+  - "@nickp60"
+maintainers:
+  - "@nickp60"

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

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+nextflow_process {
+
+    name "Test Process MIFASER"
+    script "../main.nf"
+    process "MIFASER"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "mifaser"
+    tag "untar"
+
+    setup {
+        run("UNTAR") {
+            script "modules/nf-core/untar/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    [],
+                    file(
+                        'https://github.com/nf-core/test-datasets/raw/refs/heads/funcprofiler/data/database/mifaser/GS-24-all.tar.gz',
+                        checkIfExists: true
+                    )
+                ])
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - single-end fastq") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ]
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.multi_ec,
+                    process.out.analysis,
+                    process.out.ec_counts,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - single-end fastq - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ]
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

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

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+{
+    "sarscov2 - single-end fastq - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_multi_ec.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_analysis.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_ec_count.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        "MIFASER",
+                        "mi-faser",
+                        "mifaser 1.64 (07/21/25)"
+                    ]
+                ],
+                "analysis": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_analysis.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "ec_counts": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_ec_count.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "multi_ec": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_multi_ec.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_mifaser": [
+                    [
+                        "MIFASER",
+                        "mi-faser",
+                        "mifaser 1.64 (07/21/25)"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-05-12T14:06:57.628532"
+    },
+    "sarscov2 - single-end fastq": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_multi_ec.tsv:md5,08ad0cac1771a190e63cd76a3b3ab686"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_analysis.tsv:md5,722399e3bfd7af4273b36779a111db8a"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_ec_count.tsv:md5,195e3e0db1dd8b603a7e8d91e85e480d"
+                ]
+            ],
+            {
+                "versions_mifaser": [
+                    [
+                        "MIFASER",
+                        "mi-faser",
+                        "mifaser 1.64 (07/21/25)"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-05-12T14:06:46.076826"
+    }
+}