Added new module: msisensorpro/msitumoronly

modules/nf-core/msisensorpro/msitumoronly/environment.yml

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+name: msisensorpro_msitumoronly
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::msisensor-pro=1.2.0

modules/nf-core/msisensorpro/msitumoronly/main.nf

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+process MSISENSORPRO_MSITUMORONLY {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' :
+        'biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }"
+
+    input:
+    tuple val(meta) , path(tumor), path(tumor_index), path(intervals)
+    tuple val(meta2), path (fasta)
+    tuple val(meta3), path (msisensor_baseline)
+
+    output:
+    tuple val(meta), path("${prefix}")         , emit: output_report
+    tuple val(meta), path("${prefix}_dis")     , emit: output_dis
+    tuple val(meta), path("${prefix}_all")     , emit: output_all
+    tuple val(meta), path("${prefix}_unstable"), emit: output_unstable
+    path "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args   ?: ''
+    def prefix   = task.ext.prefix ?: "${meta.id}"
+    def fasta = fasta ? "-g ${fasta}" : ""
+    def intervals = intervals ? "-e ${intervals} " : ""
+    """
+    msisensor-pro \\
+        pro \\
+        -d ${msisensor_baseline} \\
+        -t ${tumor} \\
+        ${fasta} \\
+        -o $prefix \\
+        -b ${task.cpus} \\
+        ${intervals} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        msisensor-pro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args   ?: ''
+    def prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    mkdir ${prefix}_dis
+    mkdir ${prefix}_all
+    mkdir ${prefix}_unstable
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        msisensor-pro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p')
+    END_VERSIONS
+    """
+}

modules/nf-core/msisensorpro/msitumoronly/meta.yml

@@ -0,0 +1,68 @@
+name: msisensorpro_msitumoronly
+description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input
+keywords:
+  - micro-satellite-scan
+  - msisensor-pro
+  - msi
+  - somatic
+  - tumor-only
+tools:
+  - msisensorpro:
+      description: Microsatellite Instability (MSI) detection using high-throughput sequencing data.
+      homepage: https://github.com/xjtu-omics/msisensor-pro
+      documentation: https://github.com/xjtu-omics/msisensor-pro/wiki
+      tool_dev_url: https://github.com/xjtu-omics/msisensor-pro
+      doi: "10.1016/j.gpb.2020.02.001"
+      licence: ["Custom Licence"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - tumor:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - tumor_index:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai,sai}"
+  - intervals:
+      type: file
+      description: bed file containing interval information, optional
+      pattern: "*.{bed}"
+  - fasta:
+      type: file
+      description: Reference genome
+      pattern: "*.{fasta}"
+  - msisensor_baseline:
+      type: file
+      description: File containing custom list of msi regions from a panel of normals to be used as a baseline
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - output_report:
+      type: file
+      description: File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score
+  - output_dis:
+      type: file
+      description: File containing distribution results
+  - output_all:
+      type: file
+      description: File containing all sites
+  - output_unstable:
+      type: file
+      description: File containing unstable sites
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@FriederikeHanssen"
+  - "@bounlu"
+maintainers:
+  - "@FriederikeHanssen"

modules/nf-core/msisensorpro/msitumoronly/tests/main.nf.test

@@ -0,0 +1,76 @@
+nextflow_process {
+
+    name "Test Process MSISENSORPRO_MSITUMORONLY"
+    script "../main.nf"
+    process "MSISENSORPRO_MSITUMORONLY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "msisensorpro"
+    tag "msisensorpro/msitumoronly"
+
+    test("human - cram") {
+
+        when {
+            process {
+                """
+                input[0] = [// meta map
+                        [ id:'test'],
+                        file('https://github.com/xjtu-omics/msisensor-pro/raw/c85d51030777585ad6ab669d2f4c8e46d23f4cd8/demo/data/data4test/test_tumor_sorted.cram'),
+                        //file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true),
+                        file('https://github.com/xjtu-omics/msisensor-pro/raw/c85d51030777585ad6ab669d2f4c8e46d23f4cd8/demo/data/data4test/test_tumor_sorted.cram.crai'),
+                        //file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true),
+                        []
+                    ]
+                input[1] = [ [ id:'reference' ], // meta map
+                    file('https://raw.githubusercontent.com/xjtu-omics/msisensor-pro/c85d51030777585ad6ab669d2f4c8e46d23f4cd8/demo/data/reference/reference.fa', checkIfExists: true)
+                    ]
+                input[2] = [ [ id:'baseline' ], // meta map
+                    file('https://raw.githubusercontent.com/xjtu-omics/msisensor-pro/c85d51030777585ad6ab669d2f4c8e46d23f4cd8/data/GRCh38.baseline_TCGA.tsv', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("human - cram - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [// meta map
+                        [ id:'test'],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true),
+                        []
+                    ]
+                input[1] = [ [ id:'reference' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    ]
+                input[2] = [ [ id:'baseline' ], // meta map
+                    file('https://raw.githubusercontent.com/xjtu-omics/msisensor-pro/c85d51030777585ad6ab669d2f4c8e46d23f4cd8/data/GRCh38.baseline_TCGA.tsv', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/msisensorpro/msitumoronly/tests/main.nf.test.snap

@@ -0,0 +1,84 @@
+{
+    "human - cram - stub": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "3": [
+
+                ],
+                "4": [
+
+                ],
+                "output_all": [
+
+                ],
+                "output_dis": [
+
+                ],
+                "output_report": [
+
+                ],
+                "output_unstable": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T11:32:08.214756"
+    },
+    "human - cram": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "3": [
+
+                ],
+                "4": [
+
+                ],
+                "output_all": [
+
+                ],
+                "output_dis": [
+
+                ],
+                "output_report": [
+
+                ],
+                "output_unstable": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T11:31:59.733765"
+    }
+}

modules/nf-core/msisensorpro/msitumoronly/tests/tags.yml

@@ -0,0 +1,2 @@
+msisensorpro/msitumoronly:
+  - "modules/nf-core/msisensorpro/msitumoronly/**"