Add nextdenovo to nf-core modules.

modules/nf-core/nextdenovo/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::nextdenovo=2.5.2
+  - pip=23.3.1
+  - pip:
+      - paralleltask==0.1.1
+  - python=3.8
+
+

modules/nf-core/nextdenovo/main.nf

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+process NEXTDENOVO {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/nextdenovo:2.5.2--py310h0ceaa1d_6' :
+        'biocontainers/nextdenovo:2.5.2--py310h0ceaa1d_6' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path config
+
+    output:
+    tuple val(meta), path("*.fasta.gz"), emit: fasta
+    tuple val(meta), path("*.stat")     , emit: stat
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "parallel_jobs = ${task.cpus}" >> conf.cfg
+    cat $config >> conf.cfg
+    echo ${reads} > input.fofn
+    nextDenovo \\
+        conf.cfg \\
+        input.fofn \\
+
+    gzip -c ./03.ctg_graph/nd.asm.fasta > ${prefix}.assembly.fasta.gz
+
+    mv ./03.ctg_graph/nd.asm.fasta.stat ${prefix}.assembly_info.stat
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        \$( nextDenovo --version )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo stub | gzip -c > ${prefix}.assembly.fasta.gz
+    echo contig_1 > ${prefix}.assembly_info.stat
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+    \$( nextDenovo --version )
+    END_VERSIONS
+    """
+}

modules/nf-core/nextdenovo/meta.yml

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+name: "nextdenovo"
+description: NextDenovo is a string graph-based de novo assembler for long reads (CLR,
+  HiFi and ONT). It uses a “correct-then-assemble” strategy similar to canu (no correction
+  step for PacBio HiFi reads), but requires significantly less computing resources
+  and storages
+keywords:
+  - assembly
+  - genome
+  - de novo
+  - genome assembler
+  - single molecule
+tools:
+  - "nextdenovo":
+      description: "NextDenovo is a string graph-based de novo assembler for long reads
+        (CLR, HiFi and ONT). It uses a “correct-then-assemble” strategy similar to canu
+        (no correction step for PacBio HiFi reads), but requires significantly less
+        computing resources and storages"
+      homepage: "https://github.com/fenderglass/Flye"
+      documentation: "https://nextdenovo.readthedocs.io/en/latest/"
+      tool_dev_url: "https://github.com/Nextomics/NextDenovo"
+      doi: "10.1186/s13059-024-03252-4"
+      licence: ["GPL-3.0-license"]
+      identifier: biotools:nextdenovo
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - reads:
+        type: file
+        description: Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ
+          format.
+        pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}"
+  - - config:
+        type: file
+        description: Input config file for nextDenovo
+        pattern: "*"
+output:
+  - fasta:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.fasta.gz":
+          type: file
+          description: Assembled FASTA file
+          pattern: "*.fasta.gz"
+  - stat:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.stat":
+          type: file
+          description: Extra information and statistics about resulting contigs
+          pattern: "*.stat"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@elmedjadjirayane"
+maintainers:
+  - "@elmedjadjirayane"

modules/nf-core/nextdenovo/tests/config.cfg

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+[General]
+job_type = local # local, slurm, sge, pbs, lsf
+job_prefix = nextDenovo
+task = all # all, correct, assemble
+rewrite = yes # yes/no
+deltmp = yes 
+parallel_jobs = 20 # number of tasks used to run in parallel
+input_type = raw # raw, corrected
+read_type = ont # clr, ont, hifi
+input_fofn = input.fofn
+workdir = .
+
+[correct_option]
+read_cutoff = 500
+genome_size = 100k # estimated genome size
+
+minimap2_options_raw = -t 8
+pa_correction = 3 # number of corrected tasks used to run in parallel, each corrected task requires ~TOTAL_INPUT_BASES/4 bytes of memory usage.
+correction_options = -p 15
+
+[assemble_option]
+minimap2_options_cns = -t 8 
+nextgraph_options = -a 1 -z 1 -l 1 -q 0 -N 2 -u 2 -w 3 -B 50 -C 5 -L 1 -t 50
+
+# see https://nextdenovo.readthedocs.io/en/latest/OPTION.html for a detailed introduction about all the parameters

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

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+// nf-core modules test nextdenovo
+nextflow_process {
+
+    name "Test Process NEXTDENOVO"
+    script "../main.nf"
+    process "NEXTDENOVO"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "nextdenovo"
+
+
+    test("nextdenovo_ont") {
+
+
+        when {
+            process {
+                """
+
+
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true),
+                ]
+                input[1] = file("${moduleDir}/tests/config.cfg")
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.fasta.get(0).get(1)).name,
+                    path(process.out.stat.get(0).get(1)).readLines()[1].contains("N50"),
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+
+
+}

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

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+{
+    "nextdenovo_ont": {
+        "content": [
+            "test.assembly.fasta.gz",
+            false,
+            [
+                "versions.yml:md5,7ec3ec49cbe9e0a06d3d0be767e4cc0c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-05-16T18:13:58.045501794"
+    }
+}