Add gcta/removerelatedsubjects module

modules/nf-core/gcta/removerelatedsubjects/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::gcta=1.94.1

modules/nf-core/gcta/removerelatedsubjects/main.nf

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+process GCTA_REMOVERELATEDSUBJECTS {
+    tag "${meta.id}"
+    label 'process_medium'
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46b0d05f0daa47561d87d2a9cac5e51edc2c78e26f1bbab439c688386241a274/data'
+        : 'community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9'}"
+
+    input:
+    tuple val(meta), path(grm_files)
+
+    output:
+    tuple val(meta), path("*_unrel05.grm.*"), emit: grm_files
+    tuple val(meta), path("*_unrel05.grm.id"), emit: keep_file
+    tuple val("${task.process}"), val("gcta"), eval("gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'"), emit: versions_gcta, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    gcta \\
+        --grm ${meta.id} \\
+        --grm-cutoff 0.05 \\
+        --make-grm \\
+        --out ${prefix}_unrel05 \\
+        --thread-num ${task.cpus} \\
+        ${args}
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_unrel05.grm.id
+    touch ${prefix}_unrel05.grm.bin
+    touch ${prefix}_unrel05.grm.N.bin
+    """
+}

modules/nf-core/gcta/removerelatedsubjects/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "gcta_removerelatedsubjects"
+description: Remove related individuals from a dense GRM using `gcta --grm-cutoff`
+keywords:
+  - gcta
+  - genome-wide complex trait analysis
+  - grm
+  - genetic relationship matrix
+  - genetics
+tools:
+  - "gcta":
+      description: "Genome-wide Complex Trait Analysis (GCTA) estimates genetic relationships, variance components, and association statistics from genome-wide data."
+      homepage: "https://yanglab.westlake.edu.cn/software/gcta/"
+      documentation: "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf"
+      tool_dev_url: "https://yanglab.westlake.edu.cn/software/gcta/"
+      licence: ["GPL-3.0-only"]
+      identifier: "biotools:gcta"
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy map containing dense GRM metadata.
+          `meta.id` is the required GRM basename consumed by `--grm` and must match
+          the staged dense GRM files.
+          e.g. `[ id:'tiny_dense' ]` requires
+          `tiny_dense.grm.id`, `tiny_dense.grm.bin`, and `tiny_dense.grm.N.bin`.
+    - grm_files:
+        type: file
+        description: Dense GRM file bundle with basename `${meta.id}`
+        pattern: "*.grm.*"
+        ontologies: []
+
+output:
+  grm_files:
+    - - meta:
+          type: map
+          description: |
+            Groovy map containing dense GRM metadata.
+            `meta.id` remains the dense-GRM basename contract used for `--grm`.
+      - "*_unrel05.grm.*":
+          type: file
+          description: Relatedness-filtered GRM file bundle
+          pattern: "*_unrel05.grm.*"
+          ontologies: []
+  keep_file:
+    - - meta:
+          type: map
+          description: |
+            Groovy map containing dense GRM metadata.
+            `meta.id` remains the dense-GRM basename contract used for `--grm`.
+      - "*_unrel05.grm.id":
+          type: file
+          description: Keep file of unrelated individuals emitted by GCTA
+          pattern: "*_unrel05.grm.id"
+          ontologies: []
+  versions_gcta:
+    - - "${task.process}":
+          type: string
+          description: The process the version was collected from
+      - "gcta":
+          type: string
+          description: The tool name
+      - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'":
+          type: eval
+          description: The command used to retrieve the GCTA version
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the version was collected from
+      - gcta:
+          type: string
+          description: The tool name
+      - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'":
+          type: eval
+          description: The command used to retrieve the GCTA version
+
+authors:
+  - "@lyh970817"
+maintainers:
+  - "@lyh970817"

modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process GCTA_REMOVERELATEDSUBJECTS"
+    script "../main.nf"
+    process "GCTA_REMOVERELATEDSUBJECTS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gcta"
+    tag "gcta/removerelatedsubjects"
+    tag "gcta/makegrm"
+
+    setup {
+        run("GCTA_MAKEGRM", alias: "GCTA_MAKEGRM_CONTRACT") {
+            script "../../makegrm/main.nf"
+            process {
+                """
+                file('tiny_dense.mbfile').text = 'plink_simulated\\n'
+
+                input[0] = [
+                    [ id:'tiny_dense' ],
+                    file('tiny_dense.mbfile'),
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        run("GCTA_MAKEGRM", alias: "GCTA_MAKEGRM_STUB") {
+            script "../../makegrm/main.nf"
+            process {
+                """
+                file('stub_dense.mbfile').text = 'plink_simulated\\n'
+
+                input[0] = [
+                    [ id:'stub_dense' ],
+                    file('stub_dense.mbfile'),
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+    }
+
+    test("homo_sapiens popgen - remove related individuals from dense GRM") {
+        when {
+            process {
+                """
+                input[0] = GCTA_MAKEGRM_CONTRACT.out.grm_files
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.grm_files.size() == 1 },
+                { assert process.out.keep_file.size() == 1 },
+                { assert process.out.grm_files.get(0).get(0).id == "tiny_dense" },
+                {
+                    def grm_row = process.out.grm_files.get(0)
+                    def expected_prefix = "${grm_row.get(0).id}_unrel05"
+                    assert grm_row.get(1).collect { file(it).name }.sort() == [
+                        "${expected_prefix}.grm.N.bin",
+                        "${expected_prefix}.grm.bin",
+                        "${expected_prefix}.grm.id"
+                    ]
+                    assert file(process.out.keep_file.get(0).get(1)).name == "${expected_prefix}.grm.id"
+                },
+                {
+                    assert snapshot(sanitizeOutput(process.out)).match()
+                }
+            )
+        }
+    }
+
+    test("homo_sapiens popgen - remove related individuals fails when meta.id is not GRM basename") {
+        when {
+            process {
+                """
+                input[0] = GCTA_MAKEGRM_CONTRACT.out.grm_files.map { meta, grm_files ->
+                    [[ id:'tiny_dense_mismatched' ], grm_files]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert !process.success },
+                { assert process.exitStatus != 0 }
+            )
+        }
+    }
+
+    test("homo_sapiens popgen - remove related individuals fails for malformed GRM tuple") {
+        when {
+            process {
+                """
+                input[0] = GCTA_MAKEGRM_CONTRACT.out.grm_files.map { meta, grm_files ->
+                    [[ id:meta.id ]]
+                }
+                """
+            }
+        }
+
+        then {
+            assert !process.success
+        }
+    }
+
+    test("homo_sapiens popgen - remove related individuals from dense GRM - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = GCTA_MAKEGRM_STUB.out.grm_files
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.grm_files.get(0).get(0).id == "stub_dense" },
+                {
+                    def grm_row = process.out.grm_files.get(0)
+                    def expected_prefix = "${grm_row.get(0).id}_unrel05"
+                    assert grm_row.get(1).collect { file(it).name }.sort() == [
+                        "${expected_prefix}.grm.N.bin",
+                        "${expected_prefix}.grm.bin",
+                        "${expected_prefix}.grm.id"
+                    ]
+                    assert file(process.out.keep_file.get(0).get(1)).name == "${expected_prefix}.grm.id"
+                },
+                {
+                    assert snapshot(sanitizeOutput(process.out)).match()
+                }
+            )
+        }
+    }
+}

modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test.snap

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+{
+    "homo_sapiens popgen - remove related individuals from dense GRM": {
+        "content": [
+            {
+                "grm_files": [
+                    [
+                        {
+                            "id": "tiny_dense"
+                        },
+                        [
+                            "tiny_dense_unrel05.grm.N.bin:md5,06b73ea8bae8f1e5f5d4de33dbd2c75e",
+                            "tiny_dense_unrel05.grm.bin:md5,b1f124463eecbae86840a6651eec372d",
+                            "tiny_dense_unrel05.grm.id:md5,ca8c0bded6951fdd3bf0dddc97b6df6b"
+                        ]
+                    ]
+                ],
+                "keep_file": [
+                    [
+                        {
+                            "id": "tiny_dense"
+                        },
+                        "tiny_dense_unrel05.grm.id:md5,ca8c0bded6951fdd3bf0dddc97b6df6b"
+                    ]
+                ],
+                "versions_gcta": [
+                    [
+                        "GCTA_REMOVERELATEDSUBJECTS",
+                        "gcta",
+                        "1.94.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-05-26T21:47:04.336069243"
+    },
+    "homo_sapiens popgen - remove related individuals from dense GRM - stub": {
+        "content": [
+            {
+                "grm_files": [
+                    [
+                        {
+                            "id": "stub_dense"
+                        },
+                        [
+                            "stub_dense_unrel05.grm.N.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "stub_dense_unrel05.grm.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "stub_dense_unrel05.grm.id:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "keep_file": [
+                    [
+                        {
+                            "id": "stub_dense"
+                        },
+                        "stub_dense_unrel05.grm.id:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_gcta": [
+                    [
+                        "GCTA_REMOVERELATEDSUBJECTS",
+                        "gcta",
+                        "1.94.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-05-26T21:47:35.414417262"
+    }
+}