Add module muse/sump

modules/nf-core/muse/sump/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::muse=2.1.2

modules/nf-core/muse/sump/main.nf

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+process MUSE_SUMP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/muse:2.1.2--f6ec9e78771509ff':
+        'community.wave.seqera.io/library/muse:2.1.2--e8279641c6ef8c63' }"
+
+    input:
+    tuple val(meta), path(muse_call_txt)
+    tuple val(meta2), path(ref_vcf), path(ref_vcf_tbi)
+
+    output:
+    tuple val(meta), path("*.vcf"), emit: vcf
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: '' // hands -G for WGS data and -E for WES data
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2.1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    cp $ref_vcf_tbi /tmp/
+    rm $ref_vcf_tbi
+    cp /tmp/$ref_vcf_tbi .
+    rm /tmp/$ref_vcf_tbi
+
+    MuSE \\
+        sump \\
+        $args \\
+        -I $muse_call_txt \\
+        -O ${prefix}.vcf \\
+        -n $task.cpus    \\
+        -D $ref_vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        MuSE: ${VERSION}
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2.1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        MuSE: ${VERSION}
+    END_VERSIONS
+    """
+}

modules/nf-core/muse/sump/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "muse_sump"
+description: computes tier-based cutoffs from a sample-specific error model
+keywords:
+  - genomics
+  - wgs
+  - wxs
+  - vcf
+tools:
+  - "MuSE":
+      description: "Somatic point mutation caller based on Markov substitution model
+        for molecular evolution"
+      homepage: "https://bioinformatics.mdanderson.org/public-software/muse/"
+      documentation: "https://github.com/wwylab/MuSE"
+      tool_dev_url: "https://github.com/wwylab/MuSE"
+      doi: "10.1101/gr.278456.123"
+      licence: ["https://github.com/danielfan/MuSE/blob/master/LICENSE"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - muse_call_txt:
+        type: file
+        description: single input file generated by 'MuSE call'
+        pattern: "*.MuSE.txt"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information.
+          e.g. `[ id:'test' ]`
+    - ref_vcf:
+        type: file
+        description: |
+          dbSNP vcf file that should be bgzip compressed, tabix indexed and
+          based on the same reference genome used in 'MuSE call'
+        pattern: ".vcf.gz"
+    - ref_vcf_tbi:
+        type: file
+        description: |
+          dbSNP vcf file that should be bgzip compressed, tabix indexed and
+          based on the same reference genome used in 'MuSE call'
+        pattern: ".vcf.gz.tbi"
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.vcf":
+          type: file
+          description: Identified somatic variants with tiered rankings
+          pattern: "*.vcf"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@famosab"
+maintainers:
+  - "@famosab"

modules/nf-core/muse/sump/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process MUSE_SUMP"
+    script "../main.nf"
+    process "MUSE_SUMP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "muse"
+    tag "muse/sump"
+
+    test("human - txt") {
+
+        config "./wes.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/muse/MuSE-call.chr21.hg38.paired_end.recal.MuSE.txt', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'reference' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("human - txt - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/muse/MuSE-call.chr21.hg38.paired_end.recal.MuSE.txt', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'reference' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/muse/sump/tests/main.nf.test.snap

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+{
+    "human - txt - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c09df78eaed694c69858185c8e082048"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c09df78eaed694c69858185c8e082048"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-15T10:47:30.297712631"
+    },
+    "human - txt": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,9379bf3ff498d19aea55f1e5f1f8bfe8"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c09df78eaed694c69858185c8e082048"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,9379bf3ff498d19aea55f1e5f1f8bfe8"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c09df78eaed694c69858185c8e082048"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-15T10:47:24.028424069"
+    }
+}

modules/nf-core/muse/sump/tests/tags.yml

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+muse/sump:
+  - "modules/nf-core/muse/sump/**"

modules/nf-core/muse/sump/tests/wes.config

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+process {
+    withName: 'MUSE_SUMP' {
+            ext.args   = '-E' }
+}

modules/nf-core/muse/sump/tests/wgs.config

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+process {
+    withName: 'MUSE_SUMP' {
+            ext.args   = '-G' }
+}