Clair3

modules/nf-core/clair3/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::clair3=1.0.10"

modules/nf-core/clair3/main.nf

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+process CLAIR3 {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/clair3:1.0.10--py39hd649744_1':
+        'biocontainers/clair3:1.0.10--py39hd649744_1' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(model), val(platform)
+    tuple val(meta2), path(reference)
+    tuple val(meta3), path(index)
+
+    output:
+    tuple val(meta), path("*merge_output.vcf.gz"),            emit: vcf
+    tuple val(meta), path("*merge_output.vcf.gz.tbi"),        emit: tbi
+    tuple val(meta), path("*phased_merge_output.vcf.gz"),     emit: phased_vcf, optional: true
+    tuple val(meta), path("*phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true
+    path "versions.yml",                                      emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    run_clair3.sh \\
+        --bam_fn=$bam \\
+        --ref_fn=$reference \\
+        --threads=$task.cpus \\
+        --output=. \\
+        --platform=$platform \\
+        --model=$model \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        clair3: \$(run_clair3.sh  --version |& sed '1!d ; s/Clair3 v//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}.phased_merge_output.vcf.gz
+    touch ${prefix}.phased_merge_output.vcf.gz.tbi
+    echo "" | gzip > ${prefix}.merge_output.vcf.gz
+    touch ${prefix}.merge_output.vcf.gz.tbi
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        clair3: \$(run_clair3.sh --version |& sed '1!d ; s/Clair3 v//')
+    END_VERSIONS
+    """
+}

modules/nf-core/clair3/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "clair3"
+description: Clair3 is a germline small variant caller for long-reads
+keywords:
+- germline
+- variant
+- Indel
+- SNV
+tools:
+- "clair3":
+    description: "Clair3 is a small variant caller for long-reads. Compare to PEPPER
+      (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data
+      (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally
+      four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment
+      as input for deep-learning based long-read small variant calling. Clair3 is
+      simple and modular for easy deployment and integration."
+    homepage: "https://github.com/HKU-BAL/Clair3"
+    documentation: "https://github.com/HKU-BAL/Clair3"
+    tool_dev_url: "https://github.com/HKU-BAL/Clair3"
+    doi: "10.1038/s43588-022-00387-x"
+    licence: ['BSD-3-clause']
+    identifier: biotools:clair3
+
+input:
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+      ontologies:
+      - edam: "http://edamontology.org/format_25722"
+      - edam: "http://edamontology.org/format_2573"
+      - edam: "http://edamontology.org/format_3462"
+  - bai:
+      type: file
+      description: BAM index file
+      pattern: "*.bai"
+  - model:
+      type: directory
+      description: collection of files used in a trained Clair3 model
+  - platform:
+      type: string
+      description: val in ['hifi','ont', 'ilmn'] to indicate pacbio, ONT, or illumina
+        respectively
+- - meta2:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - reference:
+      type: file
+      description: reference fasta file
+      pattern: "*.fasta"
+- - meta3:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - index:
+      type: file
+      description: reference index file
+      pattern: "*.fai"
+output:
+- vcf:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+      pattern: "*.{vcf,vcf.gz}"
+  - '*merge_output.vcf.gz':
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+      pattern: "*.{vcf,vcf.gz}"
+- tbi:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - '*merge_output.vcf.gz.tbi':
+      type: file
+      description: index for vcf files
+      pattern: "*.{vcf.tbi,vcf.tbi.gz}"
+- phased_vcf:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - '*phased_merge_output.vcf.gz':
+      type: file
+      description: phased vcf
+      pattern: "*.{vcf,vcf.gz}"
+- phased_tbi:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - '*phased_merge_output.vcf.gz.tbi':
+      type: file
+      description: index for vcf files
+      pattern: "*.{vcf.tbi,vcf.tbi.gz}"
+- versions:
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+- "@robert-a-forsyth"
+maintainers:
+- "@robert-a-forsyth"

modules/nf-core/clair3/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process CLAIR3"
+    script "../main.nf"
+    process "CLAIR3"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "clair3"
+    tag "untar"
+
+    setup {
+        run("UNTAR") {
+            script "../../../../modules/nf-core/untar/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'generic/models/clair3.hifi.tar.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+       }
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                def model_path = UNTAR.out.untar
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                ])
+                .join(UNTAR.out.untar).combine(Channel.of(['hifi']))
+                input[1] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                ]
+                input[2] = [
+                    [ id: 'test'],
+                    file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                                process.out.vcf.collect { file(it[1]).getName() },
+                                process.out.tbi.collect { file(it[1]).getName() },
+                                process.out.versions,
+                                process.out.phased_vcf.collect { file(it[1]).getName() },
+                                process.out.phased_tbi.collect { file(it[1]).getName() }).match()}
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                def model_path = UNTAR.out.untar
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                ])
+                .join(UNTAR.out.untar).combine(Channel.of(['hifi']))
+                input[1] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                ]
+                input[2] = [
+                    [ id: 'test'],
+                    file(params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                                process.out.vcf,
+                                process.out.tbi,
+                                process.out.phased_vcf,
+                                process.out.phased_tbi,
+                                process.out.versions,
+                                ).match()}
+            )
+        }
+
+    }
+
+}

modules/nf-core/clair3/tests/main.nf.test.snap

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+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    [
+                        "test.merge_output.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "test.phased_merge_output.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    [
+                        "test.merge_output.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "test.phased_merge_output.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.phased_merge_output.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.phased_merge_output.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                "versions.yml:md5,10928c13418eced076964d86249aeaf8"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-17T09:56:09.775735"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            [
+                "merge_output.vcf.gz"
+            ],
+            [
+                "merge_output.vcf.gz.tbi"
+            ],
+            [
+                "versions.yml:md5,10928c13418eced076964d86249aeaf8"
+            ],
+            [
+
+            ],
+            [
+
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-14T17:16:02.057639"
+    }
+}