Add wipertools module (#7184)

modules/nf-core/wipertools/fastqgather/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::wipertools=1.1.3"

modules/nf-core/wipertools/fastqgather/main.nf

@@ -0,0 +1,46 @@
+process WIPERTOOLS_FASTQGATHER {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/wipertools:1.1.3--pyhdfd78af_0':
+        'biocontainers/wipertools:1.1.3--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fastq_in)
+
+    output:
+    tuple val(meta), path("*_gather.fastq.gz") , emit: fastq_out
+    path "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    wipertools \\
+        fastqgather \\
+        -i $fastq_in \\
+        -o ${prefix}_gather.fastq.gz \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wipertools fastqgather: \$(wipertools fastqgather --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}_gather.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wipertools fastqgather: \$(wipertools fastqgather --version)
+    END_VERSIONS
+    """
+}

modules/nf-core/wipertools/fastqgather/meta.yml

@@ -0,0 +1,59 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "wipertools_fastqgather"
+description: A tool of the wipertools suite that merges FASTQ chunks produced by wipertools_fastqscatter
+keywords:
+  - fastq
+  - merge
+  - union
+tools:
+  - "fastqgather":
+      description:
+        "A tool of the wipertools suite that merges FASTQ chunks produced\
+        \ by wipertools_fastqscatter."
+      homepage: "https://github.com/mazzalab/fastqwiper"
+      documentation: "https://github.com/mazzalab/fastqwiper"
+      tool_dev_url: "https://github.com/mazzalab/fastqwiper"
+      doi: "no DOI available"
+      licence: ["GPL v2-or-later"]
+      identifier: ""
+      args_id: "$args"
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - fastq_in:
+        type: file
+        description: List of FASTQ chunk files to be merged
+        pattern: "*.{fastq,fastq.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1930"
+          - edam: "http://edamontology.org/format_3989"
+output:
+  - fastq_out:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*_gather.fastq.gz":
+          type: file
+          description: The resulting FASTQ file
+          pattern: "*.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930"
+            - edam: "http://edamontology.org/format_3989"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+          ontologies:
+            - edam: "http://edamontology.org/format_2330"
+authors:
+  - "@tm4zza"
+maintainers:
+  - "@mazzalab"
+  - "@tm4zza"

modules/nf-core/wipertools/fastqgather/tests/main.nf.test

@@ -0,0 +1,91 @@
+nextflow_process {
+
+    name "Test Process WIPERTOOLS_FASTQGATHER"
+    script "../main.nf"
+    process "WIPERTOOLS_FASTQGATHER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "wipertools"
+    tag "wipertools/fastqgather"
+    tag "wipertools/fastqscatter"
+
+    test("merge two gzipped fastq - fastq.gz") {
+
+        config "./nextflow.config"
+
+        setup {
+            run("WIPERTOOLS_FASTQSCATTER") {
+                script "../../fastqscatter/main.nf"
+                process {
+                    """
+                    input[0] = [
+                    [ id:'pp_' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+                    ]
+                    input[1] = 2  // number of splits
+                    """
+                }
+            }
+        }
+
+        when {
+            params {
+                module_args = '--prefix pp_'
+            }
+            process {
+                """
+                input[0] = WIPERTOOLS_FASTQSCATTER.out.chunks.map { tuple( [id: 'fastq_chunks'], it[1] ) }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("merge two gzipped fastq - fastq.gz - stub") {
+
+        options "-stub"
+        config "./nextflow.config"
+
+        setup {
+            run("WIPERTOOLS_FASTQSCATTER") {
+                script "../../fastqscatter/main.nf"
+                process {
+                    """
+                    input[0] = [
+                    [ id:'pp_' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+                    ]
+                    input[1] = 2  // number of splits
+                    """
+                }
+            }
+        }
+
+        when {
+            params {
+                module_args = '--prefix pp_'
+            }
+            process {
+                """
+                input[0] = WIPERTOOLS_FASTQSCATTER.out.chunks.map { tuple( [id: 'fastq_chunks'], it[1] ) }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/wipertools/fastqgather/tests/main.nf.test.snap

@@ -0,0 +1,68 @@
+{
+    "merge two gzipped fastq - fastq.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "fastq_chunks"
+                        },
+                        "fastq_chunks_gather.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,291a2e6d58146bfcf57b4d9ef850cbd9"
+                ],
+                "fastq_out": [
+                    [
+                        {
+                            "id": "fastq_chunks"
+                        },
+                        "fastq_chunks_gather.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,291a2e6d58146bfcf57b4d9ef850cbd9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-11T20:28:51.132317"
+    },
+    "merge two gzipped fastq - fastq.gz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "fastq_chunks"
+                        },
+                        "fastq_chunks_gather.fastq.gz:md5,eedbbe1317d4d464da30d56cff7d677e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,291a2e6d58146bfcf57b4d9ef850cbd9"
+                ],
+                "fastq_out": [
+                    [
+                        {
+                            "id": "fastq_chunks"
+                        },
+                        "fastq_chunks_gather.fastq.gz:md5,eedbbe1317d4d464da30d56cff7d677e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,291a2e6d58146bfcf57b4d9ef850cbd9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-11T20:28:40.144022"
+    }
+}

modules/nf-core/wipertools/fastqgather/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: WIPERTOOLS_FASTQGATHER {
+        ext.args = params.module_args
+    }
+}

modules/nf-core/wipertools/fastqscatter/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::wipertools=1.1.3"

modules/nf-core/wipertools/fastqscatter/main.nf

@@ -0,0 +1,55 @@
+process WIPERTOOLS_FASTQSCATTER {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/wipertools:1.1.3--pyhdfd78af_0':
+        'biocontainers/wipertools:1.1.3--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fastq)
+    val(num_splits)
+
+    output:
+    tuple val(meta), path("${out_folder}/*") , emit: chunks
+    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}"
+    def args_list   = args.tokenize()
+    out_folder      = (args_list.contains('--out_folder') ? args_list[args_list.indexOf('--out_folder')+1] : (args_list.contains('-o') ? args_list[args_list.indexOf('-o')+1] : 'chunks'))
+    """
+    wipertools \\
+        fastqscatter \\
+        -f ${fastq} \\
+        -n ${num_splits} \\
+        -p ${prefix} \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wipertools fastqscatter: \$(wipertools fastqscatter --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args        = task.ext.args ?: ''
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def args_list   = args.tokenize()
+    out_folder      = (args_list.contains('--out_folder') ? args_list[args_list.indexOf('--out_folder')+1] : (args_list.contains('-o') ? args_list[args_list.indexOf('-o')+1] : 'chunks'))
+    """
+    mkdir ${out_folder}
+    echo -e "@ERR001268.1 080821_HWI-EAS301_0002_30ALBAAXX:1:1:1090:1998/1" > ${out_folder}/${prefix}_1-of-2_suffix.fastq
+    echo -e "@ERR001268.2 080821_HWI-EAS301_0002_30ALBAAXX:1:1:1090:1998/2" > ${out_folder}/${prefix}_2-of-2_suffix.fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wipertools fastqscatter: \$(wipertools fastqscatter --version)
+    END_VERSIONS
+    """
+}