Add sylphtax taxprof module

modules/nf-core/sylphtax/taxprof/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::sylph-tax=1.1.2"

modules/nf-core/sylphtax/taxprof/main.nf

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+
+process SYLPHTAX_TAXPROF {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sylph-tax:1.1.2--pyhdfd78af_0':
+        'biocontainers/sylph-tax:1.1.2--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(sylph_results)
+    path taxonomy
+
+    output:
+    tuple val(meta), path("*.sylphmpa"), emit: taxprof_output
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    sylph-tax \\
+        taxprof \\
+        $sylph_results \\
+        $args \\
+        -o ${prefix}.sylphmpa \\
+        -t $taxonomy
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*\\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p' | head -n 1)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.sylphmpa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*\\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p' | head -n 1)
+    END_VERSIONS
+    """
+}

modules/nf-core/sylphtax/taxprof/meta.yml

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+name: sylphtax_taxprof
+description: Incorporates taxonomy into sylph metagenomic classifier
+keywords:
+- taxonomy
+- sylph
+- metagenomics
+tools:
+- sylphtax:
+    description: Integrating taxonomic information into the sylph metagenome profiler.
+    homepage: https://github.com/bluenote-1577/sylph-tax?tab=readme-ov-file
+    documentation: https://sylph-docs.github.io/sylph-tax/
+    licence: ["MIT"]
+    identifier: ''
+input:
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - sylph_results:
+      type: file
+      description: Output results from sylph classifier. The database file(s) used to create this file with sylph must be the same as those of the taxonomy input channel of this module.
+      pattern: "*.{tsv}"
+- - taxonomy:
+      type: file
+      description: A list of sylph-tax identifiers (e.g. GTDB_r220 or IMGVR_4.1).
+        Multiple taxonomy metadata files can be input. Custom taxonomy files are also
+        possible.
+output:
+- taxprof_output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+      pattern: "*{.sylphmpa}"
+  - '*.sylphmpa':
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+      pattern: "*{.sylphmpa}"
+- versions:
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+- "@sofstam"
+maintainers:
+- "@sofstam"

modules/nf-core/sylphtax/taxprof/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process SYLPHTAX_TAXPROF"
+    script "../main.nf"
+    process "SYLPHTAX_TAXPROF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sylph"
+    tag "sylph/profile"
+    tag "sylphtax"
+    tag "sylphtax/taxprof"
+
+
+    test("sarscov2 illumina single-end [fastq_gz]") {
+        setup {
+            run("SYLPH_PROFILE") {
+                script "../../../sylph/profile/main.nf"
+                process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                            [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                input[0] = SYLPH_PROFILE.out.profile_out
+                input[1] = file('https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/sylph/test_taxonomy.tsv.gz', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.taxprof_output
+                ).match() }
+            )
+        }
+
+    }
+
+    test("stub sarscov2 illumina single-end [fastq_gz]") {
+
+        options '-stub'
+
+        setup {
+            run("SYLPH_PROFILE") {
+                script "../../../sylph/profile/main.nf"
+                process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                            [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                input[0] = SYLPH_PROFILE.out.profile_out
+                input[1] = file('https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/sylph/test_taxonomy.tsv.gz', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.taxprof_output
+                ).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap

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+{
+    "stub sarscov2 illumina single-end [fastq_gz]": {
+        "content": [
+            [
+                "versions.yml:md5,976fae8d146f4f3087e2a090703f09b9"
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.sylphmpa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-13T13:27:49.708058346"
+    },
+    "sarscov2 illumina single-end [fastq_gz]": {
+        "content": [
+            [
+                "versions.yml:md5,976fae8d146f4f3087e2a090703f09b9"
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.sylphmpatest_1.fastq.gz.sylphmpa:md5,797e3463eeb9a2e8f91de9b842cd421d"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-13T13:22:19.31463228"
+    }
+}