Added samshee

modules/nf-core/samshee/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python=3.12.7
+  - pip
+  - pip: # FIXME https://github.com/nf-core/modules/issues/5814
+      - samshee==0.2.1

modules/nf-core/samshee/main.nf

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+process SAMSHEE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/65/659cdc3068a6fbce17ccb199bb3afc8600c65940743c1a0214b3bf0eed4df1a3/data' :
+        'community.wave.seqera.io/library/pip_samshee:9b655e3c18eee356' }"
+
+    input:
+    tuple val(meta), path(samplesheet)
+    path(file_schema_validator)
+
+    output:
+    tuple val(meta), path("*_formatted.csv"), emit: samplesheet
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def arg_file_schema_validator = file_schema_validator ? "--schema '{\"\$ref\": \"file:${file_schema_validator}\"}'"   : ""
+    def args = task.ext.args ?: ""
+    """
+    # Run validation command and capture output
+    python -m samshee $samplesheet \
+    $args \
+    > ${samplesheet.baseName}_formatted.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samshee: \$( python -m pip show --version samshee | grep "Version" | sed -e "s/Version: //g" )
+        python: \$( python --version | sed -e "s/Python //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${samplesheet.baseName}_formatted.csv
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samshee: \$( python -m pip show --version samshee | grep "Version" | sed -e "s/Version: //g" )
+        python: \$( python --version | sed -e "s/Python //g" )
+    END_VERSIONS
+    """
+}

modules/nf-core/samshee/meta.yml

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+name: samshee
+description: Module to validate illumina® Sample Sheet v2 files.
+keywords:
+  - samplesheet
+  - illumina
+  - bclconvert
+  - bcl2fastq
+tools:
+  - samshee:
+      description: A schema-agnostic parser and writer for illumina® sample sheets v2 and similar documents.
+      homepage: https://github.com/lit-regensburg/samshee
+      documentation: https://github.com/lit-regensburg/samshee/blob/main/README.md
+      tool_dev_url: https://github.com/lit-regensburg/samshee
+      licence: [MIT license]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', lane:1 ]
+    - samplesheet:
+        type: file
+        description: "illumina v2 samplesheet"
+        pattern: "*.{csv}"
+  - - file_schema_validator:
+        type: string
+        description: "Optional JSON file used additional samplesheet validation settings"
+output:
+  - samplesheet:
+      - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', lane:1 ]
+      - "*_formatted.csv":
+        type: file
+        description: "illumina v2 samplesheet"
+  - versions:
+      - versions.yml:
+        type: file
+        description: File containing software version
+        pattern: "versions.yml"
+authors:
+  - "@nschcolnicov"
+maintainers:
+  - "@nschcolnicov"

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

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+nextflow_process {
+
+    name "Test Process samshee"
+    script "../main.nf"
+    process "SAMSHEE"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samshee"
+
+    test("test samplesheet_v1") {
+
+        when {
+            params {
+                v1_schema = true
+            }
+            process {
+                """
+                input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/miseq_35147139/miseq_35147139_samplesheet.csv", checkIfExists: true) ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+    test("test samplesheet_v2") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NextSeq2000/SampleSheet.csv", checkIfExists: true) ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+    test("stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NextSeq2000/SampleSheet.csv", checkIfExists: true), [] ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}

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

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+{
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "lane": 1
+                        },
+                        "SampleSheet_formatted.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
+                ],
+                "samplesheet": [
+                    [
+                        {
+                            "id": "test",
+                            "lane": 1
+                        },
+                        "SampleSheet_formatted.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-15T12:33:58.766224702"
+    },
+    "test samplesheet_v1": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "lane": 1
+                        },
+                        "miseq_35147139_samplesheet_formatted.csv:md5,2a6ee5b13242aeefdeeaa98671f1ee26"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
+                ],
+                "samplesheet": [
+                    [
+                        {
+                            "id": "test",
+                            "lane": 1
+                        },
+                        "miseq_35147139_samplesheet_formatted.csv:md5,2a6ee5b13242aeefdeeaa98671f1ee26"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-15T12:30:57.470221349"
+    },
+    "test samplesheet_v2": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "lane": 1
+                        },
+                        "SampleSheet_formatted.csv:md5,9a1cac9e958256a17c7f43a8e15cb697"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
+                ],
+                "samplesheet": [
+                    [
+                        {
+                            "id": "test",
+                            "lane": 1
+                        },
+                        "SampleSheet_formatted.csv:md5,9a1cac9e958256a17c7f43a8e15cb697"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,77af0194d386117bf52aaabdf350a976"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-15T12:31:16.99133356"
+    }
+}

modules/nf-core/samshee/tests/nextflow.config

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+process {
+    withName: SAMSHEE {
+        ext.args = { params.v1_schema ? "--output-format sectioned" : "" }
+    }
+}