partial implementation of unifiedgenotyper

modules/gatk3/unifiedgenotyper/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+    // Do not publish versions.yml unless running from pytest workflow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/gatk3/unifiedgenotyper/main.nf

@@ -0,0 +1,46 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK3_UNIFIEDGENOTYPER {
+    tag '$bam'
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    // 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 (params.enable_conda ? "YOUR-TOOL-HERE" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+    } else {
+        container "quay.io/biocontainers/YOUR-TOOL-HERE"
+    }
+
+    input:
+    path bam
+    path ref
+
+    output:
+    path "*.vcf",        emit: vcf
+    path "versions.yml", emit: versions
+
+    script:
+    """
+    gatk -T UnifiedGenotyper \\
+        -R $ref \\
+        -I $bam \\
+        -o $vcf \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//' )
+    END_VERSIONS
+    """
+}

modules/gatk3/unifiedgenotyper/meta.yml

@@ -0,0 +1,41 @@
+name: gatk3_unifiedgenotyper
+description: UnifiedGenotyper from GATK 3.5, replaced by haplotyper caller. only use if needed for multivcfanalyzer
+keywords:
+  - gatk
+  - unifiedgenotyper
+  - vcf
+  - multivcfanalyzer
+tools:
+  - gatk3:
+      description: 
+        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size. Release 3.5
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/tutorials/2804-howto-Call-variants-with-the-UnifiedGenotyper
+      tool_dev_url: https://gatk.broadinstitute.org/hc/en-us
+      doi: 10.1158/1538-7445.AM2017-3590
+      licence: ['Apache-2.0']
+      
+input:
+  - bam:
+      type: file
+      description: BAM file for input
+      pattern: "*.{bam}"
+  - ref:
+      type: file
+      description: reference file used for mapping
+      pattern: "*.fa"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: unfiltered variant call format file
+      pattern: "*.{vcf}"
+
+authors:
+  - "@yocra3"

tests/config/pytest_modules.yml

@@ -390,6 +390,10 @@ freebayes:
   - modules/freebayes/**
   - tests/modules/freebayes/**
 
+gatk3/unifiedgenotyper:
+  - modules/gatk3/unifiedgenotyper/**
+  - tests/modules/gatk3/unifiedgenotyper/**
+
 gatk4/applybqsr:
   - modules/gatk4/applybqsr/**
   - tests/modules/gatk4/applybqsr/**

tests/modules/gatk3/unifiedgenotyper/main.nf

@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK3_UNIFIEDGENOTYPER } from '../../../../modules/gatk3/unifiedgenotyper/main.nf' addParams( options: [:] )
+
+workflow test_gatk3_unifiedgenotyper {
+    
+    input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+
+    GATK3_UNIFIEDGENOTYPER ( input )
+}

tests/modules/gatk3/unifiedgenotyper/test.yml

@@ -0,0 +1,10 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml gatk3/unifiedgenotyper
+- name: gatk3 unifiedgenotyper
+  command: nextflow run ./tests/modules/gatk3/unifiedgenotyper -entry test_gatk3_unifiedgenotyper -c tests/config/nextflow.config
+  tags:
+    - gatk3
+    - gatk3/unifiedgenotyper
+  files:
+    - path: output/gatk3/test.bam
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc