new module DeepMAsED

modules/nf-core/deepmased/features/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/deepmased
+  - bioconda::deepmased=0.3.1
+  - conda-forge::setuptools=78.1

modules/nf-core/deepmased/features/main.nf

@@ -0,0 +1,43 @@
+process DEEPMASED_FEATURES {
+    tag "$meta.id"
+    label 'process_high'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/deepmased:0.3.1--pyh5ca1d4c_0':
+        'quay.io/biocontainers/deepmased:0.3.1--pyh5ca1d4c_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(fasta)
+
+    output:
+    tuple val(meta), path("${prefix}_feature_file_paths.tsv"), path("*_feats.tsv"), emit: features
+    tuple val("${task.process}"), val('deepmased'), val('0.3.1'), topic: versions, emit: versions_deepmased_features
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    prefix     = task.ext.prefix ?: "${meta.id}"
+    """
+    echo -e "bam\\tfasta" > ${prefix}_file_paths.tsv
+    echo -e "${bam}\\t${fasta}" >> ${prefix}_file_paths.tsv
+
+    DeepMAsED features \\
+        ${prefix}_file_paths.tsv \\
+        -p ${task.cpus} \\
+        -o . \\
+        -n ${prefix}_feature_file_paths.tsv \\
+        ${args}
+    """
+
+    stub:
+    prefix     = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_feature_file_paths.tsv
+    touch ${prefix}_feats.tsv
+    """
+}

modules/nf-core/deepmased/features/meta.yml

@@ -0,0 +1,88 @@
+name: "deepmased_features"
+description: "DeepMAsED features subcommand: extracts alignment-based features from
+  BAM and assembly FASTA for each contig, producing feature tables used as input for
+  DeepMAsED predict."
+keywords:
+  - metagenomics
+  - assembly
+  - quality control
+  - error detection
+  - deep learning
+  - features
+tools:
+  - "deepmased":
+      description: "Deep learning for Metagenome Assembly Error Detection"
+      homepage: "https://github.com/leylabmpi/DeepMAsED"
+      documentation: "https://github.com/leylabmpi/DeepMAsED"
+      tool_dev_url: "https://github.com/leylabmpi/DeepMAsED"
+      doi: "10.1093/bioinformatics/btaa386"
+      licence:
+        - "MIT"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - bam:
+        type: file
+        description: Sorted BAM file of reads mapped to the assembly
+        pattern: "*.{bam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572"
+    - bai:
+        type: file
+        description: BAM index file
+        pattern: "*.{bai}"
+        ontologies: []
+    - fasta:
+        type: file
+        description: Assembly in FASTA format
+        pattern: "*.{fasta,fa,fna}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+output:
+  features:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}_feature_file_paths.tsv:
+          type: file
+          description: Index file listing all generated feature table files
+          pattern: "*_feature_file_paths.tsv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475"
+      - "*_feats.tsv":
+          type: file
+          description: Per-contig feature tables (one per parallel bin)
+          pattern: "*_feats.tsv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475"
+  versions_deepmased_features:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - deepmased:
+          type: string
+          description: The name of the tool
+      - 0.3.1:
+          type: string
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - deepmased:
+          type: string
+          description: The name of the tool
+      - 0.3.1:
+          type: string
+          description: The expression to obtain the version of the tool
+authors:
+  - "@SkyLexS"
+maintainers:
+  - "@SkyLexS"

modules/nf-core/deepmased/features/tests/main.nf.test

@@ -0,0 +1,66 @@
+// nf-core modules test deepmased/features
+nextflow_process {
+
+    name "Test Process DEEPMASED_FEATURES"
+    script "../main.nf"
+    process "DEEPMASED_FEATURES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "deepmased"
+    tag "deepmased/features"
+    tag "deepmased_features"
+
+    test("sarscov2 [fasta] - paired-end sorted bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', 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() },
+                { assert path(process.out.features[0][1]).exists() },
+                { assert path(process.out.features[0][1]).readLines().size() > 1 }
+            )
+        }
+
+    }
+
+    test("sarscov2 [fasta] - paired-end sorted bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', 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/deepmased/features/tests/main.nf.test.snap

@@ -0,0 +1,92 @@
+{
+    "sarscov2 [fasta] - paired-end sorted bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_feature_file_paths.tsv:md5,4eceace937a13c4318294cee72cb4320",
+                        "test.paired_end.sorted_feats.tsv:md5,81bc5e8ac16d47ea7fde1c07a92fbba3"
+                    ]
+                ],
+                "1": [
+                    [
+                        "DEEPMASED_FEATURES",
+                        "deepmased",
+                        "0.3.1"
+                    ]
+                ],
+                "features": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_feature_file_paths.tsv:md5,4eceace937a13c4318294cee72cb4320",
+                        "test.paired_end.sorted_feats.tsv:md5,81bc5e8ac16d47ea7fde1c07a92fbba3"
+                    ]
+                ],
+                "versions_deepmased_features": [
+                    [
+                        "DEEPMASED_FEATURES",
+                        "deepmased",
+                        "0.3.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
+        },
+        "timestamp": "2026-05-13T09:59:49.966230332"
+    },
+    "sarscov2 [fasta] - paired-end sorted bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_feature_file_paths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test_feats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "DEEPMASED_FEATURES",
+                        "deepmased",
+                        "0.3.1"
+                    ]
+                ],
+                "features": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_feature_file_paths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test_feats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_deepmased_features": [
+                    [
+                        "DEEPMASED_FEATURES",
+                        "deepmased",
+                        "0.3.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
+        },
+        "timestamp": "2026-05-13T10:04:26.105533827"
+    }
+}

modules/nf-core/deepmased/predict/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/deepmased
+  - bioconda::deepmased=0.3.1
+  - conda-forge::setuptools=78.1

modules/nf-core/deepmased/predict/main.nf

@@ -0,0 +1,38 @@
+process DEEPMASED_PREDICT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/deepmased:0.3.1--pyh5ca1d4c_0':
+        'quay.io/biocontainers/deepmased:0.3.1--pyh5ca1d4c_0' }"
+
+    input:
+    tuple val(meta), path(feature_file_table), path(feature_files)
+
+    output:
+    tuple val(meta), path("*_deepmased_predictions.tsv"), emit: predictions
+    tuple val("${task.process}"), val('deepmased'), val('0.3.1'), topic: versions, emit: versions_deepmased_predict
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: '--cpu-only'
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    DeepMAsED predict \\
+        ${feature_file_table} \\
+        --n-procs ${task.cpus} \\
+        --save-name ${prefix}_deepmased \\
+        ${args}
+    """
+
+    stub:
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_deepmased_predictions.tsv
+    """
+}