Imported module from branch trgt

modules/nf-core/trgt/plot/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::trgt=1.2.0"

modules/nf-core/trgt/plot/main.nf

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+process TRGT_PLOT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0':
+        'biocontainers/trgt:1.2.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta) , path(bam), path(bai), path(vcf), path(tbi), val(repeat_id)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(repeats)
+
+    output:
+    tuple val(meta), path("*.{png,pdf,svg}"), emit: plot
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}_${repeat_id}"
+    // If user didn't specify an output path, plot to PNG
+    def output_arg = args.contains("--image") || args.contains("-o") ? "" : "--image ${prefix}.png"
+
+    """
+    trgt plot \\
+        $args \\
+        --genome ${fasta} \\
+        --repeats ${repeats} \\
+        --spanning-reads ${bam} \\
+        --vcf ${vcf} \\
+        --repeat-id ${repeat_id} \\
+        $output_arg
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
+    END_VERSIONS
+    """
+}

modules/nf-core/trgt/plot/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "trgt_plot"
+description: Visualize tandem repeats genotyped by TRGT
+keywords:
+  - trgt
+  - repeat expansion
+  - plotting
+  - pacbio
+  - genomics
+tools:
+  - "trgt":
+      description: "Tandem repeat genotyping and visualization from PacBio HiFi data"
+      homepage: "https://github.com/PacificBiosciences/trgt"
+      documentation: "https://github.com/PacificBiosciences/trgt/blob/main/docs/tutorial.md"
+      tool_dev_url: "https://github.com/PacificBiosciences/trgt"
+      doi: "10.1038/s41587-023-02057-3"
+      licence:
+        ["Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: "Sorted reads spanning tandem repeat from TRGT output"
+        pattern: "*.bam"
+    - bai:
+        type: file
+        description: "Index for reads"
+        pattern: "*.bai"
+    - vcf:
+        type: file
+        description: "Sorted tandem repeat genotypes called by TRGT"
+        pattern: "*.vcf.gz"
+    - tbi:
+        type: file
+        description: "Index for genotypes"
+        pattern: "*.{tbi,csi}"
+    - repeat_id:
+        type: string
+        description: "ID of tandem repeat to plot"
+  - - meta2:
+        type: map
+        description: |
+          Groovy map containing reference information
+          e.g. `[ id: 'genome' ]`
+    - fasta:
+        type: file
+        description: "FASTA reference file"
+        pattern: "*.{fasta,fa,fna}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy map containing reference information
+          e.g. `[ id: 'genome' ]`
+    - fai:
+        type: file
+        description: "Index for FASTA file"
+        pattern: "*.fai"
+  - - meta4:
+        type: map
+        description: |
+          Groovy map containing repeat information
+          e.g. `[ id: 'repeats' ]`
+    - repeats:
+        type: file
+        description: "BED file with repeat coordinates and structure"
+        pattern: "*.bed"
+
+output:
+  - plot:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.{png,pdf,svg}":
+          type: file
+          description: "Plot of region and reads spanning tandem repeat"
+          pattern: "*.{png,pdf,svg}"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@Schmytzi"
+maintainers:
+  - "@Schmytzi"

modules/nf-core/trgt/plot/tests/main.nf.test

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+// nf-core modules test trgt/plot
+nextflow_process {
+
+    name "Test Process TRGT_PLOT"
+    script "../main.nf"
+    process "TRGT_PLOT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "trgt"
+    tag "trgt/plot"
+    tag "trgt/genotype"
+    tag "samtools/faidx"
+    tag "samtools/sort"
+    tag "samtools/index"
+    tag "bcftools/sort"
+    tag "gunzip"
+
+    setup {
+        run("GUNZIP"){
+            script "../../../gunzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id : 'chr22' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22_chr22_KI270734v1_random/sequence/genome.fa.gz', checkIfExists: true)
+                ]
+            """
+            }
+        }
+        run("SAMTOOLS_FAIDX"){
+            script "../../../samtools/faidx/main.nf"
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = [[],[]]
+                """
+            }
+        }
+        run("TRGT_GENOTYPE"){
+            script "../../genotype/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    'XX'
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+        run("SAMTOOLS_SORT"){
+            script "../../../samtools/sort/main.nf"
+            process {
+                """
+                input[0] = TRGT_GENOTYPE.out.bam
+                input[1] = [[],[]]
+                """
+            }
+        }
+        run("SAMTOOLS_INDEX"){
+            script "../../../samtools/index/main.nf"
+            process {
+                """
+                input[0] = SAMTOOLS_SORT.out.bam
+                """
+            }
+        }
+        run("BCFTOOLS_SORT"){
+            script "../../../bcftools/sort/main.nf"
+            process {
+                """
+                input[0] = TRGT_GENOTYPE.out.vcf
+                """
+            }
+        }
+    }
+
+    test("homo sapiens - [bam, bai, vcf, TEST], fasta, fai, bed") {
+        when {
+            process {
+                """
+                input[0] = SAMTOOLS_SORT.out.bam
+                            .join(SAMTOOLS_INDEX.out.bai)
+                            .join(BCFTOOLS_SORT.out.vcf)
+                            .join(BCFTOOLS_SORT.out.tbi)
+                            .map { tuple -> tuple + 'TEST' }
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo sapiens - [bam, bai, vcf, TEST], fasta, fai, bed - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = SAMTOOLS_SORT.out.bam
+                            .join(SAMTOOLS_INDEX.out.bai)
+                            .join(BCFTOOLS_SORT.out.vcf)
+                            .join(BCFTOOLS_SORT.out.tbi)
+                            .map { tuple -> tuple + 'TEST' }
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/trgt/plot/tests/main.nf.test.snap

@@ -0,0 +1,68 @@
+{
+    "homo sapiens - [bam, bai, vcf, TEST], fasta, fai, bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24cc939a0b88728bae8a2102feaf542c"
+                ],
+                "plot": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24cc939a0b88728bae8a2102feaf542c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-14T16:10:13.150678363"
+    },
+    "homo sapiens - [bam, bai, vcf, TEST], fasta, fai, bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_TEST.png:md5,32a2b217628e72817d7ec848a648029d"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24cc939a0b88728bae8a2102feaf542c"
+                ],
+                "plot": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_TEST.png:md5,32a2b217628e72817d7ec848a648029d"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24cc939a0b88728bae8a2102feaf542c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-14T16:11:37.679432214"
+    }
+}

modules/nf-core/trgt/plot/tests/nextflow.config

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+process {
+    withName: "BCFTOOLS_SORT" {
+        ext.args = "--write-index=tbi --output-type z"
+        ext.prefix = "sorted_"
+    }
+}