nf-core · KevinMLanderos · May 14, 2025 · May 16, 2025 · May 16, 2025
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,3 +1,4 @@
 {
-    "nextflow.formatting.harshilAlignment": true
+    "nextflow.formatting.harshilAlignment": true,
+    "nextflow.telemetry.enabled": false
 }
diff --git a/modules/nf-core/gemma/kinshipmatrix/environment.yml b/modules/nf-core/gemma/kinshipmatrix/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::gemma=0.98.5"
diff --git a/modules/nf-core/gemma/kinshipmatrix/main.nf b/modules/nf-core/gemma/kinshipmatrix/main.nf
@@ -0,0 +1,49 @@
+process GEMMA_KINSHIPMATRIX {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gemma:0.98.5--ha36d3ea_0':
+        'biocontainers/gemma/0.98.5--ha36d3ea_0' }"
+
+    input:
+    tuple val(meta), path(genotype)
+    tuple val(meta2), path(phenotype)
+
+    output:
+    tuple val(meta), path("output/${meta.id}.out.cXX.txt"), emit: matrix
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    gemma \\
+        $args \\
+        -g $genotype \\
+        -p $phenotype  \\
+        -gk \\
+        -o ${meta.id}.out
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gemma: \$(gemma --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir output
+    touch output/${meta.id}.out.cXX.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gemma: \$(gemma --version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gemma/kinshipmatrix/meta.yml b/modules/nf-core/gemma/kinshipmatrix/meta.yml
@@ -0,0 +1,64 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "gemma_kinshipmatrix"
+description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
+keywords:
+  - matrix
+  - lmms
+  - gwas
+tools:
+  - "gemma":
+      description: "Linear mixed models (LMMs) for genome-wide association (GWA)"
+      homepage: "https://github.com/genetics-statistics/GEMMA"
+      documentation: "https://github.com/genetics-statistics/GEMMA"
+      tool_dev_url: "https://github.com/genetics-statistics/GEMMA"
+      doi: "https://doi.org/10.1038/ng.2310"
+      licence: ["GPL v3"]
+      identifier: biotools:gemma
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+
+    - genotype:
+        type: file
+        description: genotype_matrix file
+        pattern: "*.txt"
+
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+
+    - phenotype:
+        type: file
+        description: phenotype file
+        pattern: "*.txt"
+
+output:
+  - heat_map:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.cXX.txt":
+          type: file
+          description: kinship matrix
+          pattern: "*cXX.txt"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@chriswyatt1"
+maintainers:
+  - "@chriswyatt1"
diff --git a/modules/nf-core/gemma/kinshipmatrix/test/main.nf.test b/modules/nf-core/gemma/kinshipmatrix/test/main.nf.test
@@ -0,0 +1,76 @@
+nextflow_process {
+
+    name "Test Process GEMMA_KINSHIPMATRIX"
+    script "../main.nf"
+    process "GEMMA_KINSHIPMATRIX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gemma"
+    tag "gemma/kinshipmatrix"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("gwas - vcf - pheno") {
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file( "https://raw.githubusercontent.com/genetics-statistics/GEMMA/master/example/mouse_hs1940.geno.txt.gz", checkIfExists: true)
+
+                ]
+                input[1] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file( "https://raw.githubusercontent.com/genetics-statistics/GEMMA/master/example/mouse_hs1940.pheno.txt", checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("gwas - vcf - pheno - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file( "https://raw.githubusercontent.com/genetics-statistics/GEMMA/master/example/mouse_hs1940.geno.txt.gz", checkIfExists: true)
+
+                ]
+                input[1] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file( "https://raw.githubusercontent.com/genetics-statistics/GEMMA/master/example/mouse_hs1940.pheno.txt", checkIfExists: true),
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gemma/kinshipmatrix/test/main.nf.test.snap b/modules/nf-core/gemma/kinshipmatrix/test/main.nf.test.snap
@@ -0,0 +1,128 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,02383d9d5046a267d81f99463df55749"
+                ],
+                "matrix": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,02383d9d5046a267d81f99463df55749"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-05-14T16:34:56.015094848"
+    },
+    "gwas - vcf - pheno - stub": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "matrix": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-05-14T17:51:24.26939259"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.out.cXX.txt:md5,83fbef03ff6c4e7e89bebd52ce9d11a6",
+                            "test.out.log.txt:md5,f7eccba3f5e053669b3fb2b8c5f635e7"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,02383d9d5046a267d81f99463df55749"
+                ],
+                "matrix": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.out.cXX.txt:md5,83fbef03ff6c4e7e89bebd52ce9d11a6",
+                            "test.out.log.txt:md5,f7eccba3f5e053669b3fb2b8c5f635e7"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,02383d9d5046a267d81f99463df55749"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-05-14T16:34:38.506668318"
+    },
+    "gwas - vcf - pheno": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "matrix": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-05-14T17:51:16.641698027"
+    }
+}
diff --git a/modules/nf-core/gemma/lmm/environment.yml b/modules/nf-core/gemma/lmm/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::gemma=0.98.5"
diff --git a/modules/nf-core/gemma/lmm/main.nf b/modules/nf-core/gemma/lmm/main.nf
@@ -0,0 +1,54 @@
+process GEMMA_LMM {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gemma:0.98.5--ha36d3ea_0':
+        'community.wave.seqera.io/library/gemma:0.98.5--87bf3eea4b1ea0ad' }"
+
+    input:
+    tuple val(meta), path(genotype)
+    tuple val(meta2), path(phenotype)
+    tuple val(meta3), path(annot)
+    tuple val(meta4), path(cXX)
+
+    output:
+    tuple val(meta), path("output/${meta.id}.out.assoc.txt"), emit: matrix
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    gemma \\
+        $args \\
+        -g $genotype \\
+        -p $phenotype  \\
+        -n 4 \\
+        -a $annot \\
+        -k $cXX \\
+        -lmm \\
+        -o ${meta.id}.out
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gemma: \$(gemma --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir output
+    touch output/${meta.id}.out.assoc.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gemma: \$(gemma --version)
+    END_VERSIONS
+    """
+}