Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912)

* remove params statement

* add manta/somatic module

* fix strelka target bed thing

* removing checksums should make this pass

* Update modules/manta/somatic/main.nf

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* fix indentation

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

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+    // Do not publish versions.yml unless running from pytest workflow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

@@ -0,0 +1,67 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process MANTA_SOMATIC {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${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::manta=1.6.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1"
+    } else {
+        container "quay.io/biocontainers/manta:1.6.0--h9ee0642_1"
+    }
+
+    input:
+    tuple val(meta), path(cram_normal), path(crai_normal), path(cram_tumor), path(crai_tumor)
+    path fasta
+    path fai
+    path target_bed
+    path target_bed_tbi
+
+    output:
+    tuple val(meta), path("*.candidate_small_indels.vcf.gz")     , emit: candidate_small_indels_vcf
+    tuple val(meta), path("*.candidate_small_indels.vcf.gz.tbi") , emit: candidate_small_indels_vcf_tbi
+    tuple val(meta), path("*.candidate_sv.vcf.gz")               , emit: candidate_sv_vcf
+    tuple val(meta), path("*.candidate_sv.vcf.gz.tbi")           , emit: candidate_sv_vcf_tbi
+    tuple val(meta), path("*.diploid_sv.vcf.gz")                 , emit: diploid_sv_vcf
+    tuple val(meta), path("*.diploid_sv.vcf.gz.tbi")             , emit: diploid_sv_vcf_tbi
+    tuple val(meta), path("*.somatic_sv.vcf.gz")                 , emit: somatic_sv_vcf
+    tuple val(meta), path("*.somatic_sv.vcf.gz.tbi")             , emit: somatic_sv_vcf_tbi
+    path "versions.yml"                                          , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def options_manta = target_bed ? "--exome --callRegions $target_bed" : ""
+
+    """
+    configManta.py \
+        --tumorBam $cram_tumor \
+        --normalBam $cram_normal \
+        --reference $fasta \
+        $options_manta \
+        --runDir manta
+
+    python manta/runWorkflow.py -m local -j $task.cpus
+
+    mv manta/results/variants/candidateSmallIndels.vcf.gz     ${prefix}.candidate_small_indels.vcf.gz
+    mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi ${prefix}.candidate_small_indels.vcf.gz.tbi
+    mv manta/results/variants/candidateSV.vcf.gz              ${prefix}.candidate_sv.vcf.gz
+    mv manta/results/variants/candidateSV.vcf.gz.tbi          ${prefix}.candidate_sv.vcf.gz.tbi
+    mv manta/results/variants/diploidSV.vcf.gz                ${prefix}.diploid_sv.vcf.gz
+    mv manta/results/variants/diploidSV.vcf.gz.tbi            ${prefix}.diploid_sv.vcf.gz.tbi
+    mv manta/results/variants/somaticSV.vcf.gz                ${prefix}.somatic_sv.vcf.gz
+    mv manta/results/variants/somaticSV.vcf.gz.tbi            ${prefix}.somatic_sv.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( configManta.py --version )
+    END_VERSIONS
+    """
+}

modules/manta/somatic/meta.yml

@@ -0,0 +1,103 @@
+name: manta_somatic
+description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
+keywords:
+  - somatic
+  - wgs
+  - wxs
+  - panel
+  - vcf
+  - structural variants
+  - small indels
+tools:
+  - manta:
+      description: Structural variant and indel caller for mapped sequencing data
+      homepage: https://github.com/Illumina/manta
+      documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md
+      tool_dev_url: https://github.com/Illumina/manta
+      doi: "10.1093/bioinformatics/btv710"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - cram_normal:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - crai_normal:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai,sai}"
+  - cram_tumor:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - crai_tumor:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai,sai}"
+  - fasta:
+      type: file
+      description: Genome reference FASTA file
+      pattern: "*.{fa,fasta}"
+  - fai:
+      type: file
+      description: Genome reference FASTA index file
+      pattern: "*.{fa.fai,fasta.fai}"
+  - target_bed:
+      type: file
+      description: BED file containing target regions for variant calling
+      pattern: "*.{bed}"
+  - target_bed_tbi:
+      type: file
+      description: Index for BED file containing target regions for variant calling
+      pattern: "*.{bed.tbi}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - candidate_small_indels_vcf:
+      type: file
+      description: Gzipped VCF file containing variants
+      pattern: "*.{vcf.gz}"
+  - candidate_small_indels_vcf_tbi:
+      type: file
+      description: Index for gzipped VCF file containing variants
+      pattern: "*.{vcf.gz.tbi}"
+  - candidate_sv_vcf:
+      type: file
+      description: Gzipped VCF file containing variants
+      pattern: "*.{vcf.gz}"
+  - candidate_sv_vcf_tbi:
+      type: file
+      description: Index for gzipped VCF file containing variants
+      pattern: "*.{vcf.gz.tbi}"
+  - diploid_sv_vcf:
+      type: file
+      description: Gzipped VCF file containing variants
+      pattern: "*.{vcf.gz}"
+  - diploid_sv_vcf_tbi:
+      type: file
+      description: Index for gzipped VCF file containing variants
+      pattern: "*.{vcf.gz.tbi}"
+  - somatic_sv_vcf:
+      type: file
+      description: Gzipped VCF file containing variants
+      pattern: "*.{vcf.gz}"
+  - somatic_sv_vcf_tbi:
+      type: file
+      description: Index for gzipped VCF file containing variants
+      pattern: "*.{vcf.gz.tbi}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@FriederikeHanssen"

modules/strelka/germline/main.nf

@@ -23,17 +23,19 @@ process STRELKA_GERMLINE {
     path  fasta
     path  fai
     path  target_bed
+    path  target_bed_tbi
+
 
     output:
     tuple val(meta), path("*variants.vcf.gz")    , emit: vcf
     tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi
     tuple val(meta), path("*genome.vcf.gz")      , emit: genome_vcf
     tuple val(meta), path("*genome.vcf.gz.tbi")  , emit: genome_vcf_tbi
-    path  "versions.yml"                         , emit: versions
+    path "versions.yml"                          , emit: versions
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def regions  = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
+    def regions  = target_bed ? "--exome --callRegions ${target_bed}" : ""
     """
     configureStrelkaGermlineWorkflow.py \\
         --bam $bam \\
@@ -50,7 +52,7 @@ process STRELKA_GERMLINE {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$( configureStrelkaGermlineWorkflow.py --version )
+        ${getSoftwareName(task.process)}: \$( configureStrelkaSomaticWorkflow.py --version )
     END_VERSIONS
     """
 }

modules/strelka/somatic/main.nf

@@ -34,7 +34,7 @@ process STRELKA_SOMATIC {
 
     script:
     def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
+    def options_strelka = target_bed ? "--exome --callRegions ${target_bed}" : ""
     """
     configureStrelkaSomaticWorkflow.py \\
         --tumor $cram_tumor \\

tests/config/pytest_modules.yml

@@ -678,6 +678,10 @@ maltextract:
   - modules/maltextract/**
   - tests/modules/maltextract/**
 
+manta/somatic:
+  - modules/manta/somatic/**
+  - tests/modules/manta/somatic/**
+
 mash/sketch:
   - modules/mash/sketch/**
   - tests/modules/mash/sketch/**

tests/modules/manta/somatic/main.nf

@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MANTA_SOMATIC } from '../../../../modules/manta/somatic/main.nf' addParams( options: [:] )
+
+workflow test_manta_somatic {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
+    ]
+
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bed     = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
+    bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
+
+    MANTA_SOMATIC ( input, fasta, fai, bed, bed_tbi )
+}

tests/modules/manta/somatic/test.yml

@@ -0,0 +1,18 @@
+- name: manta somatic test_manta_somatic
+  command: nextflow run tests/modules/manta/somatic -entry test_manta_somatic -c tests/config/nextflow.config
+  tags:
+    - manta/somatic
+    - manta
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.diploid_sv.vcf.gz
+    - path: output/manta/test.diploid_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/manta/test.somatic_sv.vcf.gz
+    - path: output/manta/test.somatic_sv.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905

tests/modules/strelka/germline/main.nf

@@ -5,30 +5,32 @@ nextflow.enable.dsl = 2
 include { STRELKA_GERMLINE } from '../../../../modules/strelka/germline/main.nf' addParams( options: [:] )
 
 workflow test_strelka_germline {
-    input = [ 
+    input = [
         [ id:'test'], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
     ]
-    
-    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    targets = []
-    
-    STRELKA_GERMLINE ( input, fasta, fai, targets )
+
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    target_bed     = []
+    target_bed_tbi = []
+
+    STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
 }
 
 workflow test_strelka_germline_target_bed {
-    input = [ 
+    input = [
         [ id:'test'], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
     ]
 
-    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai     = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+    fasta          = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai            = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    target_bed     = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
+    target_bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
 
-    STRELKA_GERMLINE ( input, fasta, fai, targets )
+    STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
 }
 

tests/modules/strelka/germline/test.yml

@@ -1,20 +1,21 @@
-- name: strelka germline
-  command: nextflow run ./tests/modules/strelka/germline -entry test_strelka_germline -c tests/config/nextflow.config
+- name: strelka germline test_strelka_germline
+  command: nextflow run tests/modules/strelka/germline -entry test_strelka_germline -c tests/config/nextflow.config
   tags:
     - strelka
     - strelka/germline
   files:
-    - path: output/strelka/test.variants.vcf.gz
-    - path: output/strelka/test.variants.vcf.gz.tbi
     - path: output/strelka/test.genome.vcf.gz
     - path: output/strelka/test.genome.vcf.gz.tbi
-- name: strelka germline target bed
-  command: nextflow run ./tests/modules/strelka/germline -entry test_strelka_germline_target_bed -c tests/config/nextflow.config
+    - path: output/strelka/test.variants.vcf.gz
+    - path: output/strelka/test.variants.vcf.gz.tbi
+
+- name: strelka germline test_strelka_germline_target_bed
+  command: nextflow run tests/modules/strelka/germline -entry test_strelka_germline_target_bed -c tests/config/nextflow.config
   tags:
     - strelka
     - strelka/germline
   files:
-    - path: output/strelka/test.variants.vcf.gz
-    - path: output/strelka/test.variants.vcf.gz.tbi
     - path: output/strelka/test.genome.vcf.gz
     - path: output/strelka/test.genome.vcf.gz.tbi
+    - path: output/strelka/test.variants.vcf.gz
+    - path: output/strelka/test.variants.vcf.gz.tbi