Filtermutectcalls (#796)

* first commit with files for filtermutectcalls initialised

* found missing test file that needs to be resolved

* saving config changes

* fixing pytest_module conflict

* finished module, just needs repository side tests added

* test data added, versions file updated

* modified to emit correct versions file

* Update main.nf

* Update test_data.config

* updated test script

* fixed main.nf

* Update main.nf

* Update main.nf

* removed whitespace from test script

* Update test_data.config

* Update .gitignore

* Update test_data.config

* tests changed to new names, main script edited to match comments on learnreads pr

* Update meta.yml

* Apply suggestions from code review

* Update main.nf

* Apply suggestions from code review

* Apply suggestions from code review

* Update main.nf

* Update main.nf

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/gatk4/filtermutectcalls/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/gatk4/filtermutectcalls/main.nf

@@ -0,0 +1,65 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_FILTERMUTECTCALLS {
+    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 ? "bioconda::gatk4=4.2.0.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+    } else {
+        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+    }
+
+    input:
+    tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)
+    path fasta
+    path fastaidx
+    path dict
+
+    output:
+    tuple val(meta), path("*.vcf.gz")            , emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi")        , emit: tbi
+    tuple val(meta), path("*.filteringStats.tsv"), emit: stats
+    path "versions.yml"                          , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    def orientationbias_options = ''
+    if (orientationbias) {
+        orientationbias_options = '--orientation-bias-artifact-priors ' + orientationbias.join(' --orientation-bias-artifact-priors ')
+    }
+
+    def segmentation_options = ''
+    if (segmentation) {
+        segmentation_options = '--tumor-segmentation ' + segmentation.join(' --tumor-segmentation ')
+    }
+
+    def contamination_options = contaminationest ? " --contamination-estimate ${contaminationest} " : ''
+    if (contaminationfile) {
+        contamination_options = '--contamination-table ' + contaminationfile.join(' --contamination-table ')
+    }
+    """
+    gatk FilterMutectCalls \\
+        -R $fasta \\
+        -V $vcf \\
+        $orientationbias_options \\
+        $segmentation_options \\
+        $contamination_options \\
+        -O ${prefix}.vcf.gz \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/gatk4/filtermutectcalls/meta.yml

@@ -0,0 +1,84 @@
+name: gatk4_filtermutectcalls
+description: |
+        Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.
+keywords:
+  - filtermutectcalls
+  - mutect2
+  - gatk4
+  - filtervcf
+tools:
+  - gatk4:
+      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.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      doi: 10.1158/1538-7445.AM2017-3590
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - vcf:
+      type: file
+      description: compressed vcf file of mutect2calls
+      pattern: "*.vcf.gz"
+  - tbi:
+      type: file
+      description: Index of vcf file
+      pattern: "*vcf.gz.tbi"
+  - stats:
+      type: file
+      description: Stats file that pairs with output vcf file
+      pattern: "*vcf.gz.stats"
+  - orientationbias:
+      type: list
+      description: files containing artifact priors for input vcf. Optional input.
+      pattern: "*.artifact-prior.tar.gz"
+  - segmentation:
+      type: list
+      description: tables containing segmentation information for input vcf. Optional input.
+      pattern: "*.segmentation.table"
+  - contaminationfile:
+      type: list
+      description: table(s) containing contamination contamination data for input vcf. Optional input, takes priority over contaminationest.
+      pattern: "*.contamination.table"
+  - contaminationest:
+      type: val
+      description: estimation of contamination value as a double. Optional input, will only be used if contaminationfile is not specified.
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+  - fastaidx:
+      type: file
+      description: Index of reference fasta file
+      pattern: "fasta.fai"
+  - dict:
+      type: file
+      description: GATK sequence dictionary
+      pattern: "*.dict"
+
+output:
+  - vcf:
+      type: file
+      description: file containing filtered mutect2 calls.
+      pattern: "*.vcf.gz"
+  - tbi:
+      type: file
+      description: tbi file that pairs with vcf.
+      pattern: "*.vcf.gz.tbi"
+  - stats:
+      type: file
+      description: file containing statistics of the filtermutectcalls run.
+      pattern: "*.filteringStats.tsv"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@GCJMackenzie"

tests/config/pytest_modules.yml

@@ -410,6 +410,10 @@ gatk4/fastqtosam:
   - modules/gatk4/fastqtosam/**
   - tests/modules/gatk4/fastqtosam/**
 
+gatk4/filtermutectcalls:
+  - modules/gatk4/filtermutectcalls/**
+  - tests/modules/gatk4/filtermutectcalls/**
+
 gatk4/getpileupsummaries:
   - modules/gatk4/getpileupsummaries/**
   - tests/modules/gatk4/getpileupsummaries/**

tests/modules/gatk4/filtermutectcalls/main.nf

@@ -0,0 +1,65 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/gatk4/filtermutectcalls/main.nf' addParams( options: [suffix:'.filtered'] )
+
+workflow test_gatk4_filtermutectcalls_base {
+
+    input = [ 
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
+        [],
+        [],
+        [],
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict )
+}
+
+workflow test_gatk4_filtermutectcalls_with_files {
+
+    input = [ 
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_artifact_prior_tar_gz'], checkIfExists: true) ],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_segmentation_table'], checkIfExists: true) ],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_contamination_table'], checkIfExists: true) ],
+        []
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict )
+}
+
+workflow test_gatk4_filtermutectcalls_use_val {
+
+    input = [ 
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true),
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_artifact_prior_tar_gz'], checkIfExists: true) ],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_segmentation_table'], checkIfExists: true) ],
+        [],
+        '20.0'
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_FILTERMUTECTCALLS ( input, fasta, fastaidx, dict )
+}

tests/modules/gatk4/filtermutectcalls/test.yml

@@ -0,0 +1,35 @@
+- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_base
+  command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_base -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/filtermutectcalls
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
+      md5sum: 98e1b87a52999eb8f429ef4a7877eb3f
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+      md5sum: d88d2b745c9226ddf284e3494db8b9d2
+
+- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_with_files
+  command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_with_files -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/filtermutectcalls
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
+      md5sum: 98e1b87a52999eb8f429ef4a7877eb3f
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+      md5sum: d88d2b745c9226ddf284e3494db8b9d2
+
+- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_use_val
+  command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_use_val -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/filtermutectcalls
+  files:
+    - path: output/gatk4/test.filtered.vcf.gz
+    - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv
+      md5sum: 98e1b87a52999eb8f429ef4a7877eb3f
+    - path: output/gatk4/test.filtered.vcf.gz.tbi
+      md5sum: d88d2b745c9226ddf284e3494db8b9d2