Test PR for CI check

assets/samplesheet.csv

@@ -1,3 +1,2 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+id,vcf,pheno,cov
+test,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/data/data_shrink_combined_4500/chr1_to_22_and_X.vcf.bgz,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/gwas/data/data_phenotypes_and_covariates/example1.pheno,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/gwas/data/data_phenotypes_and_covariates/example1.covar

assets/schema_input.json

@@ -7,27 +7,31 @@
     "items": {
         "type": "object",
         "properties": {
-            "sample": {
+            "id": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
-            "fastq_1": {
+            "vcf": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
-            "fastq_2": {
+            "pheno": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+            },
+            "cov": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["id", "vcf", "pheno"]
     }
 }

conf/modules.config

@@ -27,4 +27,11 @@ process {
         ]
     }
 
+    withName: 'PLINK_GWAS' {
+        ext.args   = '--allow-no-sex --linear'
+        publishDir = [
+            path: { "${params.outdir}/plink_gwas" },
+            mode: params.publish_dir_mode
+        ]
+    }
 }

modules.json

@@ -9,6 +9,16 @@
                         "branch": "master",
                         "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
+                    },
+                    "plink/gwas": {
+                        "branch": "master",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "installed_by": ["modules"]
+                    },
+                    "plink/vcf": {
+                        "branch": "master",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"]
                     }
                 }
             },

modules/local/qqman/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::r-qqman=0.1.4"

modules/local/qqman/main.nf

@@ -0,0 +1,55 @@
+process QQMAN {
+    tag "$meta.id"
+    label 'process_single'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/r-qqman:0.1.4--r341h6115d3f_2':
+        'biocontainers/r-qqman:0.1.4--r341h6115d3f_2' }"
+
+    input:
+    tuple val(meta), path(assoc)
+
+    output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    tuple val(meta), path("*.png"), emit: bam
+    // TODO nf-core: List additional required output channels/values here
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    ls
+    Rscript qqman.R \\
+    -i mydata.assoc \\
+    -m my_manhattan.png \\
+    -q my_qq.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        qqman: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+
+    stub:
+    // def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        qqman: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+}

modules/local/qqman/meta.yml

@@ -0,0 +1,69 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "qqman"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "qqman":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "Create Q-Q and manhattan plots for GWAS data from PLINK results."
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "None"
+      doi: ""
+      licence: ['GPL v3']
+      identifier: 
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+  ## TODO nf-core: Delete / customise this example input
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_2573"
+          - edam: "http://edamontology.org/format_3462"
+
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  - bam:
+  #Only when we have meta
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+  ## TODO nf-core: Delete / customise this example output
+    - "*.bam":
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_2573"
+          - edam: "http://edamontology.org/format_3462"
+
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@FernandoDuarteF"
+maintainers:
+  - "@FernandoDuarteF"

modules/local/qqman/qqman.R

@@ -0,0 +1,44 @@
+
+# Load required packages
+suppressPackageStartupMessages({
+  library(argparse)
+  library(qqman)
+})
+
+# ---- ARGUMENT PARSING ----
+parser <- ArgumentParser(description = "Run qqman on a PLINK .assoc file")
+
+parser$add_argument("-i", "--input", required = TRUE,
+                    help = "Input PLINK .assoc file")
+parser$add_argument("-m", "--manhattan", default = "manhattan_plot.png",
+                    help = "Output filename for Manhattan plot [default: manhattan_plot.png]")
+parser$add_argument("-q", "--qq", default = "qq_plot.png",
+                    help = "Output filename for Q-Q plot [default: qq_plot.png]")
+
+args <- parser$parse_args()
+
+# ---- LOAD DATA ----
+assoc_data <- read.table(args$input, header = TRUE)
+
+# Validate required columns
+required_cols <- c("CHR", "BP", "SNP", "P")
+missing_cols <- setdiff(required_cols, colnames(assoc_data))
+if (length(missing_cols) > 0) {
+  stop(paste("Missing required columns in .assoc file:", paste(missing_cols, collapse = ", ")))
+}
+
+# ---- PLOTTING ----
+
+# Manhattan plot
+png(args$manhattan, width = 1000, height = 600)
+manhattan(assoc_data, main = "Manhattan Plot")
+dev.off()
+
+# Q-Q plot
+png(args$qq, width = 600, height = 600)
+qq(assoc_data$P, main = "Q-Q Plot")
+dev.off()
+
+cat("Plots saved:\n")
+cat("  Manhattan plot:", args$manhattan, "\n")
+cat("  Q-Q plot:", args$qq, "\n")

modules/local/qqman/tests/main.nf.test

@@ -0,0 +1,73 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test qqman
+nextflow_process {
+
+    name "Test Process QQMAN"
+    script "../main.nf"
+    process "QQMAN"
+
+    tag "modules"
+    tag "modules_"
+    tag "qqman"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - 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(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}