Smudgeplot all

modules/nf-core/smudgeplot/all/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fastk=1.2
+  - bioconda::smudgeplot=0.5.3

modules/nf-core/smudgeplot/all/main.nf

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+process SMUDGEPLOT_ALL {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/32/320648514649f5379149eed196b162e0d409b785f670ddecdf948febd6917377/data':
+        'community.wave.seqera.io/library/fastk_smudgeplot:1352fed7dbb39646' }"
+
+    input:
+    tuple val(meta), path(smu)
+
+    output:
+    tuple val(meta), path("*.png"), emit: png
+    tuple val(meta), path("*_centralities.txt"), emit: centrality_txt
+    tuple val(meta), path("*.smudge_report.tsv"), emit: smudge_report
+    tuple val(meta), path("*.sma"), emit: sma
+    tuple val("${task.process}"), val('smudgeplot'), eval('smudgeplot -v |& sed "s/.*v//"'), emit: versions_smudgeplot, topic: versions
+    // FASTK does not report version to cli
+    tuple val("${task.process}"), val('fastk'), val('1.2'), emit: versions_fastk, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args    = task.ext.args     ?: ''
+    def prefix  = task.ext.prefix   ?: "${meta.id}"
+
+    // Export HOME to avoid issues with MATPLOTLIB needing a
+    // writable config directory
+    """
+    export HOME=\$PWD/nxf_home
+
+    smudgeplot all \\
+        ${args} \\
+        -o ${prefix} \\
+        ${smu}
+    """
+
+    stub:
+    def prefix  = task.ext.prefix   ?: "${meta.id}"
+    """
+    touch ${prefix}.smu
+    """
+}

modules/nf-core/smudgeplot/all/meta.yml

@@ -0,0 +1,121 @@
+name: "smudgeplot_all"
+description: Generating smudgeplot k-mer inference plots
+keywords:
+  - Smudgeplot
+  - reference-free
+  - kmer
+  - plots
+tools:
+  - "smudgeplot":
+      description: "Generating smudgeplot kmer counts"
+      homepage: "https://github.com/KamilSJaron/smudgeplot"
+      tool_dev_url: "https://github.com/KamilSJaron/smudgeplot"
+      licence: ["https://github.com/KamilSJaron/smudgeplot/blob/master/LICENSE.md"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - smu:
+        type: file
+        description: Smudgeplot kmer coverage flat file
+        pattern: "*.smu"
+        ontologies: []
+
+output:
+  png:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.png":
+          type: file
+          description: Collection of output PNG files
+          pattern: "*.png"
+          ontologies:
+            - edam: http://edamontology.org/format_3603 # PNG
+  centrality_txt:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_centralities.txt":
+          type: file
+          description: Centrality of kmers text file
+          pattern: "*_centralities.txt"
+          ontologies:
+            - edam: http://edamontology.org/format_2330
+  smudge_report:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.smudge_report.tsv":
+          type: file
+          description: Full smudgeplot report of smudges
+          pattern: "*.smudge_report.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  sma:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.sma":
+          type: file
+          description: Smudgeplot Kmer coverage file
+          pattern: "*.sma"
+          ontologies: []
+
+  versions_smudgeplot:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - smudgeplot:
+          type: string
+          description: The name of the tool
+      - smudgeplot -v |& sed "s/.*v//":
+          type: string
+          description: The expression to obtain the version of the tool
+  versions_fastk:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - fastk:
+          type: string
+          description: Name of the tool
+      - "1.2":
+          type: string
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - smudgeplot:
+          type: string
+          description: The name of the tool
+      - smudgeplot -v |& sed "s/.*v//":
+          type: string
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - fastk:
+          type: string
+          description: Name of the tool
+      - "1.2":
+          type: string
+          description: The expression to obtain the version of the tool
+
+authors:
+  - "@DLBPointon"
+maintainers:
+  - "@DLBPointon"

modules/nf-core/smudgeplot/all/tests/main.nf.test

@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process SMUDGEPLOT_ALL"
+    script "../main.nf"
+    process "SMUDGEPLOT_ALL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "smudgeplot"
+    tag "smudgeplot/all"
+    tag "fastk/fastk"
+
+    setup {
+        run("FASTK_FASTK") {
+            script "modules/nf-core/fastk/fastk/main.nf"
+            config "./nextflow.config"
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file("https://tolit.cog.sanger.ac.uk/test-data/Acropora_cervicornis/genomic_data/m84093_241116_151316_s2.hifi_reads.bc2028.subset.fasta.gz", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        run("SMUDGEPLOT_HETMERS") {
+            script "modules/nf-core/smudgeplot/hetmers/main.nf"
+            config "./nextflow.config"
+            process {
+                """
+                input[0] = FASTK_FASTK.out.ktab
+                """
+            }
+        }
+    }
+
+    test("Acropora_cervicornis - reads") {
+
+        when {
+            process {
+                """
+                input[0] = SMUDGEPLOT_HETMERS.out.kmer_cov
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+}

modules/nf-core/smudgeplot/all/tests/main.nf.test.snap

@@ -0,0 +1,31 @@
+{
+    "Acropora_cervicornis - reads": {
+        "content": [
+            {
+                "centrality_txt": [
+
+                ],
+                "png": [
+
+                ],
+                "sma": [
+
+                ],
+                "smudge_report": [
+
+                ],
+                "versions_fastk": [
+
+                ],
+                "versions_smudgeplot": [
+
+                ]
+            }
+        ],
+        "timestamp": "2026-09-15T12:16:22.673108219",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    }
+}

modules/nf-core/smudgeplot/all/tests/nextflow.config

@@ -0,0 +1,9 @@
+process {
+    withName: "FASTK_FASTK" {
+        ext.args        = { "-k31 -t -P." }
+    }
+
+    withName: "SMUDGEPLOT_HETMERS" {
+        ext.args        = { "-L 12 -t2 -tmp ./ --verbose" }
+    }
+}

modules/nf-core/smudgeplot/hetmers/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fastk=1.2
+  - bioconda::smudgeplot=0.5.3

modules/nf-core/smudgeplot/hetmers/main.nf

@@ -0,0 +1,43 @@
+process SMUDGEPLOT_HETMERS {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/32/320648514649f5379149eed196b162e0d409b785f670ddecdf948febd6917377/data':
+        'community.wave.seqera.io/library/fastk_smudgeplot:1352fed7dbb39646' }"
+
+    input:
+    tuple val(meta), path(fastk_table, stageAs: "ktab_dir/*")
+
+    output:
+    tuple val(meta), path("*.smu"), emit: kmer_cov
+    tuple val("${task.process}"), val('smudgeplot'), eval('smudgeplot -v |& sed "s/.*v//"'), emit: versions_smudgeplot, topic: versions
+    // FASTK does not report version to cli
+    tuple val("${task.process}"), val('fastk'), val('1.2'), emit: versions_fastk, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args    = task.ext.args     ?: ''
+    def prefix  = task.ext.prefix   ?: "${meta.id}"
+
+    // Export HOME to avoid issues with MATPLOTLIB needing a
+    // writable config directory
+    """
+    export HOME=\$PWD/nxf_home
+
+    smudgeplot hetmers \\
+        ${args} \\
+        -o ${prefix} \\
+        ${fastk_table.find { path -> path.toString().endsWith(".ktab") }}
+
+    """
+
+    stub:
+    def prefix  = task.ext.prefix   ?: "${meta.id}"
+    """
+    touch ${prefix}.smu
+    """
+}