add gcta/gsmr tool

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

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+process GCTA_GSMR {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gcta:1.94.1--h9ee0642_0':
+        'biocontainers/gcta:1.94.1--h9ee0642_0' }"
+
+    input:
+    tuple val(meta) , path(exposure)
+    tuple val(meta2), path(outcome)
+    path(reference)
+
+    output:
+    tuple val(meta), val(meta2), path("*.log")          , emit: log
+    tuple val(meta), val(meta2), path("*.gsmr")         , emit: gsmr
+    tuple val(meta), val(meta2), path("*.eff_plot.gz")  , emit: eff_plot, optional: true
+    tuple val(meta), val(meta2), path("*.mono.badsnsps"), emit: mono_badsnps, optional: true
+    path "versions.yml"                                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}_${meta2.id}"
+    """
+    echo "${meta.id} ${exposure}" > ${meta.id}.input.txt
+    echo "${meta2.id} ${outcome}" > outcome.txt
+    file=\$(ls $reference | sed 's/\\.[^.]*\$//')
+    echo "${reference}/\$file" | head -n1 > reference.txt
+
+    gcta  \\
+        $args \\
+        --mbfile reference.txt  \\
+        --gsmr-file ${meta.id}.input.txt outcome.txt \\
+        --out "${prefix}"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+            gcta: \$(gcta 2>&1 | awk '/no analysis has been launched/ {exit 0} {print}' | sed -n 's/.*version \\(v[0-9.]*\\).*/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}_${meta2.id}"
+    """
+    touch ${prefix}.log
+    touch ${prefix}.gsmr
+    touch ${prefix}.mono.badsnps
+    echo "" | gzip > ${prefix}.eff_plot.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+            gcta: \$(gcta 2>&1 | awk '/no analysis has been launched/ {exit 0} {print}' | sed -n 's/.*version \\(v[0-9.]*\\).*/\\1/p')
+    END_VERSIONS
+    """
+}

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

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+name: gcta_gsmr
+description: Module that performs a Mendelian Randomization analysis with summary
+  data and plink bfile.
+keywords:
+  - Mendelian Randomization
+  - GWAS
+  - gsmr
+tools:
+  - gcta:
+      description: |
+        GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of phenotypic variance explained
+        by all genome-wide SNPs for complex traits.
+      homepage: https://yanglab.westlake.edu.cn/software/gcta
+      documentation: https://yanglab.westlake.edu.cn/software/gcta/
+      tool_dev_url: https://github.com/jianyangqt/gcta
+      doi: 10.1038/s41467-017-02317-2
+      licence: ["GPL v3"]
+      identifier: biotools:gcta
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information for exposure
+          e.g. [ id:'sample1' ]
+    - exposure:
+        type: file
+        description: Exposure data file for GSMR analysis
+        pattern: "*.txt"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information for outcome
+          e.g. [ id:'sample2' ]
+    - outcome:
+        type: file
+        description: Outcome data file for GSMR analysis
+        pattern: "*.txt"
+        ontologies: []
+  - - reference:
+        type: file
+        description: Reference files (BED, BIM, FAM) for GCTA analysis
+        pattern: "*.{bed,bim,fam}"
+        multiple: true
+        ontologies: []
+output:
+  - log:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: |
+            Groovy Map containing sample information for outcome
+      - "*.log":
+          type: file
+          description: Log file from GSMR analysis
+          pattern: "*.log"
+  - gsmr:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: |
+            Groovy Map containing sample information for outcome
+      - "*.gsmr":
+          type: file
+          description: Result file from GSMR analysis
+          pattern: "*.gsmr"
+  - eff_plot:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: |
+            Groovy Map containing sample information for outcome
+      - "*.eff_plot.gz":
+          type: file
+          description: Effect plot file from GSMR analysis (gzipped)
+          pattern: "*.eff_plot.gz"
+          optional: true
+  - mono_badsnps:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information for exposure
+      - meta2:
+          type: map
+          description: |
+            Groovy Map containing sample information for outcome
+      - "*.mono.badsnsps":
+          type: file
+          description: Bad SNPs file from GSMR analysis
+          pattern: "*.mono.badsnps"
+          optional: true
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@juliaapolonio"
+maintainers:
+  - "@juliaapolonio"

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

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+nextflow_process {
+
+    name "Test Process GCTA_GSMR"
+    script "../main.nf"
+    process "GCTA_GSMR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gcta"
+    tag "gcta/gsmr"
+
+    test("homo_sapiens - gsmr") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_exposure' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats.tsv")
+                ]
+                input[1] = [
+                    [ id:'test_outcome' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats_copy.tsv")
+                ]
+
+                // Stage individual files
+                def bedFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bed")
+                def bimFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bim")
+                def famFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.fam")
+
+                // Create a folder and move files into it
+                def referenceDir = file("reference")
+                referenceDir.mkdirs()
+                bedFile.copyTo(referenceDir.resolve("reference.bed"))
+                bimFile.copyTo(referenceDir.resolve("reference.bim"))
+                famFile.copyTo(referenceDir.resolve("reference.fam"))
+
+                // Pass the folder as input
+                input[2] = referenceDir
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                process.out.gsmr,
+                process.out.eff_plot,
+                process.out.mono_badsnps,
+                process.out.versions
+            ).match()
+            assert path(process.out.versions.get(0)).text.contains("GSMR")
+        }
+
+    }
+
+    test("homo_sapiens - gsmr - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_exposure' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats.tsv")
+                ]
+                input[1] = [
+                    [ id:'test_outcome' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats_copy.tsv")
+                ]
+
+                // Stage individual files
+                def bedFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bed")
+                def bimFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.bim")
+                def famFile = file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/bfile/bfile.fam")
+
+                // Create a folder and move files into it
+                def referenceDir = file("reference")
+                referenceDir.mkdirs()
+                bedFile.copyTo(referenceDir.resolve("reference.bed"))
+                bimFile.copyTo(referenceDir.resolve("reference.bim"))
+                famFile.copyTo(referenceDir.resolve("reference.fam"))
+
+                // Pass the folder as input
+                input[2] = referenceDir
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                process.out.gsmr,
+                process.out.eff_plot,
+                process.out.mono_badsnps,
+                process.out.versions
+            ).match()
+
+        }
+
+    }
+
+}

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

@@ -0,0 +1,44 @@
+{
+    "homo_sapiens - gsmr": {
+        "content": [
+            [
+                "test_exposure_test_outcome.gsmr:md5,f137c763773522ea37849d919f6de9aa"
+            ],
+            [
+
+            ],
+            [
+                "test_exposure_test_outcome.mono.badsnps:md5,0fe7dcfd9384c40361e7009ed28098cc"
+            ],
+            [
+                "versions.yml:md5,9d63b9cb692159dbd3c08b55eca5212b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-26T16:57:12.009292265"
+    },
+    "homo_sapiens - gsmr - stub": {
+        "content": [
+            [
+                "test_exposure_test_outcome.gsmr:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "test_exposure_test_outcome.eff_plot.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+            ],
+            [
+                "test_exposure_test_outcome.mono.badsnps:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                "versions.yml:md5,9d63b9cb692159dbd3c08b55eca5212b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-26T16:57:20.670192583"
+    }
+}