Imputeme (#882)

* first commit with imputeme as a module. Extensive re-write of imputeme-code, resulting in release v1.0.7 that is runnable in the next-flow framework.


Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>

modules/imputeme/vcftoprs/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/imputeme/vcftoprs/main.nf

@@ -0,0 +1,60 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process IMPUTEME_VCFTOPRS {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "YOUR-TOOL-HERE" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/imputeme/vv1.0.7_cv1/imputeme_vv1.0.7_cv1.img"
+    } else {
+        container "biocontainers/imputeme:vv1.0.7_cv1"
+    }
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    path "versions.yml"            , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    #!/usr/bin/env Rscript
+
+    #Set configuration - either from options.args or from defaults
+    source("/imputeme/code/impute-me/functions.R")
+    if(file.exists('$options.args')){
+        set_conf("set_from_file",'$options.args')
+    }else{
+        set_conf("set_from_file", "/imputeme/code/impute-me/template/nextflow_default_configuration.R")
+    }
+
+    #main run
+    return_message <- prepare_individual_genome('$vcf',overrule_vcf_checks=T)
+    uniqueID <- sub(' </b>.+\$','',sub('^.+this run is <b> ','',return_message))
+    convert_vcfs_to_simple_format(uniqueID=uniqueID)
+    crawl_for_snps_to_analyze(uniqueIDs=uniqueID)
+    run_export_script(uniqueIDs=uniqueID)
+    file.copy(paste0("./",uniqueID,"/",uniqueID,"_data.json"),"output.json")
+
+    #version export. Have to hardcode process name and software name because
+    #won't run inside an R-block
+    version_file_path="versions.yml"
+    f <- file(version_file_path,"w")
+    writeLines("IMPUTEME_VCFTOPRS:", f)
+    writeLines(paste0(" imputeme: ", sub("^v","",get_conf("version"))),f)
+    close(f)
+
+    """
+
+}

modules/imputeme/vcftoprs/meta.yml

@@ -0,0 +1,41 @@
+name: imputeme_vcftoprs
+description: inputs a VCF-file with whole genome DNA sequencing. Outputs a JSON with polygenic risk scores.
+keywords:
+  - PRS, VCF
+tools:
+  - imputeme:
+      description:
+      homepage: www.impute.me
+      documentation: https://hub.docker.com/repository/docker/lassefolkersen/impute-me
+      tool_dev_url: https://github.com/lassefolkersen/impute-me
+      doi: "https://doi.org/10.3389/fgene.2020.00578"
+      licence: LGPL3
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ vcf:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: vcf file
+      pattern: "*.{vcf}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: json containing Z-scores for all calculated PRS
+      pattern: "*.{json}"
+
+authors:
+  - "@lassefolkersen"

tests/config/pytest_modules.yml

@@ -609,6 +609,10 @@ homer/makeucscfile:
   - modules/homer/makeucscfile/**
   - tests/modules/homer/makeucscfile/**
 
+imputeme/vcftoprs:
+  - modules/imputeme/vcftoprs/**
+  - tests/modules/imputeme/vcftoprs/**
+
 idr:
   - modules/idr/**
   - tests/modules/idr/**

tests/config/test_data.config

@@ -119,6 +119,8 @@ params {
                 gnomad_r2_1_1_vcf_gz_tbi                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
                 mills_and_1000g_indels_vcf_gz                  = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
                 mills_and_1000g_indels_vcf_gz_tbi              = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
+                syntheticvcf_short_vcf_gz                      = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
+                syntheticvcf_short_vcf_gz_tbi                  = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
                 index_salmon                                   = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
                 repeat_expansions                              = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
             }

tests/modules/imputeme/vcftoprs/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IMPUTEME_VCFTOPRS } from '../../../../modules/imputeme/vcftoprs/main.nf' addParams( options: [:]  )
+
+workflow test_imputeme_vcftoprs {
+    
+    input = [ 
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
+    ]
+
+    IMPUTEME_VCFTOPRS ( input )
+}

tests/modules/imputeme/vcftoprs/test.yml

@@ -0,0 +1,8 @@
+- name: imputeme vcftoprs test_imputeme_vcftoprs
+  command: nextflow run tests/modules/imputeme/vcftoprs -entry test_imputeme_vcftoprs -c tests/config/nextflow.config
+  tags:
+    - imputeme
+    - imputeme/vcftoprs
+  files:
+    - path: output/imputeme/output.json
+      contains: [ 'type_2_diabetes_32541925":{"GRS":[24.01]' ]