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FernandoDuarteFFernandoDuarteF
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Added qqman
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‎modules/local/qqman/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- "bioconda::r-qqman=0.1.4"

‎modules/local/qqman/main.nf‎

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

‎modules/local/qqman/meta.yml‎

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

‎modules/local/qqman/qqman.R‎

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

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

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

‎workflows/gwas.nf‎

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@@ -10,6 +10,7 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi
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include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_gwas_pipeline'
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include { PLINK_VCF } from '../modules/nf-core/plink/vcf/main'
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include { PLINK_GWAS } from '../modules/nf-core/plink/gwas/main'
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include { QQMAN } from '../modules/local/qqman/main'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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[[],[]],
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)
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QQMAN (
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PLINK_GWAS.out.qassoc
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)
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//
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// Collate and save software versions
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//

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