Merge freebayes subtools (#1015)

* feat: merge freebayes subtools

* fix: typo

* assess comments from review

* fix: path to module

modules/freebayes/main.nf

@@ -4,7 +4,7 @@ include { initOptions; saveFiles; getProcessName; getSoftwareName } from './func
 params.options = [:]
 options        = initOptions(params.options)
 
-process FREEBAYES_GERMLINE {
+process FREEBAYES {
     tag "$meta.id"
     label 'process_low'
     publishDir "${params.outdir}",
@@ -19,7 +19,7 @@ process FREEBAYES_GERMLINE {
     }
 
     input:
-    tuple val(meta), path(input), path(input_index)
+    tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index)
     path fasta
     path fai
     path targets
@@ -33,6 +33,7 @@ process FREEBAYES_GERMLINE {
 
     script:
     def prefix           = options.suffix ? "${meta.id}${options.suffix}"  : "${meta.id}"
+    def input            = input_2        ? "${input_1} ${input_2}"        : "${input_1}"
     def targets_file     = targets        ? "--target ${targets}"          : ""
     def samples_file     = samples        ? "--samples ${samples}"         : ""
     def populations_file = populations    ? "--populations ${populations}" : ""
@@ -48,7 +49,7 @@ process FREEBAYES_GERMLINE {
             $populations_file \\
             $cnv_file \\
             $options.args \\
-            $input  > ${prefix}.vcf
+            $input > ${prefix}.vcf
 
         gzip --no-name ${prefix}.vcf
 

modules/freebayes/meta.yml

@@ -1,11 +1,14 @@
-name: freebayes_germline
+name: freebayes
 description: A haplotype-based variant detector
 keywords:
   - variant caller
   - SNP
   - genotyping
-  - variant calling
+  - somatic variant calling
+  - germline variant calling
+  - bacterial variant calling
   - bayesian
+
 tools:
   - freebayes:
       description: Bayesian haplotype-based polymorphism discovery and genotyping
@@ -73,6 +76,8 @@ output:
       type: file
       description: Compressed VCF file
       pattern: "*.vcf.gz"
+
 authors:
   - "@maxibor"
   - "@FriederikeHanssen"
+  - "@maxulysse"

modules/freebayes/somatic/functions.nf

@@ -1,78 +0,0 @@
-//
-//  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/freebayes/somatic/main.nf

@@ -1,74 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getProcessName; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process FREEBAYES_SOMATIC {
-    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::freebayes=1.3.5" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3"
-    } else {
-        container "quay.io/biocontainers/freebayes:1.3.5--py38ha193a2f_3"
-    }
-
-    input:
-    tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor)
-    path fasta
-    path fai
-    path targets
-    path samples
-
-    output:
-    tuple val(meta), path("*.vcf.gz")   , emit: vcf
-    path  "versions.yml"                , emit: versions
-
-    script:
-    def prefix           = options.suffix ? "${meta.id}${options.suffix}"  : "${meta.id}"
-    def targets_file     = targets        ? "--target ${targets}"          : ""
-    def samples_file     = samples        ? "--samples ${samples}"         : ""
-
-    if (task.cpus > 1) {
-        """
-        freebayes-parallel \\
-            <(fasta_generate_regions.py ${fasta}.fai 10000) ${task.cpus} \\
-            -f $fasta \\
-            $targets_file \\
-            $samples_file \\
-            $options.args \\
-            $input_tumor \\
-            $input_normal  > ${prefix}.vcf
-
-        gzip --no-name ${prefix}.vcf
-
-        cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
-        END_VERSIONS
-        """
-
-    } else {
-        """
-        freebayes \\
-            -f $fasta \\
-            $targets_file \\
-            $samples_file \\
-            $options.args \\
-            $input_tumor \\
-            $input_normal  > ${prefix}.vcf
-
-        gzip --no-name ${prefix}.vcf
-
-        cat <<-END_VERSIONS > versions.yml
-        ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
-        END_VERSIONS
-        """
-    }
-}

modules/freebayes/somatic/meta.yml

@@ -1,66 +0,0 @@
-name: freebayes_somatic
-description: A haplotype-based variant detector
-keywords:
-  - variant caller
-  - SNP
-  - genotyping
-  - somatic variant calling
-  - bayesian
-
-tools:
-  - freebayes:
-      description: Bayesian haplotype-based polymorphism discovery and genotyping
-      homepage: https://github.com/freebayes/freebayes
-      documentation: https://github.com/freebayes/freebayes
-      tool_dev_url: https://github.com/freebayes/freebayes
-      doi: "arXiv:1207.3907"
-      licence: ['MIT']
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
-  - input_index:
-      type: file
-      description: BAM/CRAM/SAM index file
-      pattern: "*.bam.bai"
-  - fasta:
-      type: file
-      description: reference fasta file
-      pattern: ".{fa,fa.gz,fasta,fasta.gz}"
-  - fai:
-      type: file
-      description: reference fasta file index
-      pattern: "*.fai"
-  - targets:
-      type: file
-      description: Optional - Limit analysis to targets listed in this BED-format FILE.
-      pattern: "*.bed"
-  - samples:
-      type: file
-      description: Optional - Limit analysis to samples listed (one per line) in the FILE.
-      pattern: "*.txt"
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.{version.txt}"
-  - vcf:
-      type: file
-      description: Compressed VCF file
-      pattern: "*.vcf.gz"
-
-authors:
-  - "@FriederikeHanssen"

tests/config/pytest_modules.yml

@@ -410,13 +410,9 @@ flash:
   - modules/flash/**
   - tests/modules/flash/**
 
-freebayes/germline:
+freebayes:
-  - modules/freebayes/germline/**
+  - modules/freebayes/**
-  - tests/modules/freebayes/germline/**
+  - tests/modules/freebayes/**
-
-freebayes/somatic:
-  - modules/freebayes/somatic/**
-  - tests/modules/freebayes/somatic/**
 
 gatk4/applybqsr:
   - modules/gatk4/applybqsr/**

tests/modules/freebayes/germline/main.nf

@@ -1,51 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FREEBAYES_GERMLINE } from '../../../../modules/freebayes/germline/main.nf' addParams( options: [:] )
-
-workflow test_freebayes {
-
-    input = [ [ id:'test', single_end:false ], // 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)]
-    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai         = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    targets = []
-    samples = []
-    populations = []
-    cnv = []
-
-    FREEBAYES_GERMLINE ( input, fasta, fai, targets, samples, populations, cnv)
-}
-
-workflow test_freebayes_bed {
-
-    input = [ [ id:'test', single_end:false ], // 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)]
-    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)
-    samples     = []
-    populations = []
-    cnv         = []
-
-    FREEBAYES_GERMLINE ( input, fasta, fai, targets, samples, populations, cnv)
-}
-
-workflow test_freebayes_cram {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_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)
-    targets = []
-    samples = []
-    populations = []
-    cnv = []
-
-    FREEBAYES_GERMLINE ( input, fasta, fai, targets, samples, populations, cnv)
-}

tests/modules/freebayes/germline/test.yml

@@ -1,26 +0,0 @@
-- name: freebayes germline test_freebayes
-  command: nextflow run tests/modules/freebayes/germline -entry test_freebayes -c tests/config/nextflow.config
-  tags:
-    - freebayes
-    - freebayes/germline
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: 1ec210ad27514c7a4140c924dc66d979
-
-- name: freebayes germline test_freebayes_bed
-  command: nextflow run tests/modules/freebayes/germline -entry test_freebayes_bed -c tests/config/nextflow.config
-  tags:
-    - freebayes
-    - freebayes/germline
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: e8923cccd5dac196f72d3d3997a60706
-
-- name: freebayes germline test_freebayes_cram
-  command: nextflow run tests/modules/freebayes/germline -entry test_freebayes_cram -c tests/config/nextflow.config
-  tags:
-    - freebayes
-    - freebayes/germline
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: cb57a3ed154618e3aa4a5272fcfb7521

tests/modules/freebayes/main.nf

@@ -0,0 +1,95 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FREEBAYES } from '../../../modules/freebayes/main.nf' addParams( options: [:] )
+
+workflow test_freebayes {
+
+    input = [ [ id:'test', single_end:false ], // 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),
+              [],
+              []
+            ]
+    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai         = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    targets     = []
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
+}
+
+workflow test_freebayes_bed {
+
+    input = [ [ id:'test', single_end:false ], // 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),
+              [],
+              []
+            ]
+    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)
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
+}
+
+workflow test_freebayes_cram {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_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)
+    targets     = []
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
+}
+
+workflow test_freebayes_somatic {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], 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)
+    targets     = []
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
+}
+
+workflow test_freebayes_somatic_cram_intervals {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_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)
+    targets     = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+    samples     = []
+    populations = []
+    cnv         = []
+
+    FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
+}

tests/modules/freebayes/somatic/main.nf

@@ -1,37 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { FREEBAYES_SOMATIC } from '../../../../modules/freebayes/somatic/main.nf' addParams( options: [:] )
-
-workflow test_freebayes {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], 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)
-    targets = []
-    samples = []
-
-    FREEBAYES_SOMATIC ( input, fasta, fai, targets, samples)
-}
-
-workflow test_freebayes_intervals {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_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)
-    targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-    samples = []
-
-    FREEBAYES_SOMATIC ( input, fasta, fai, targets, samples)
-}

tests/modules/freebayes/somatic/test.yml

@@ -1,17 +0,0 @@
-- name: freebayes somatic test_freebayes
-  command: nextflow run tests/modules/freebayes/somatic -entry test_freebayes -c tests/config/nextflow.config
-  tags:
-    - freebayes/somatic
-    - freebayes
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: 1c47d02f27ec5918558c8688ce6e7780
-
-- name: freebayes somatic test_freebayes_intervals
-  command: nextflow run tests/modules/freebayes/somatic -entry test_freebayes_intervals -c tests/config/nextflow.config
-  tags:
-    - freebayes/somatic
-    - freebayes
-  files:
-    - path: output/freebayes/test.vcf.gz
-      md5sum: 5b8a12666bde63746dcec7afcd3ef789

tests/modules/freebayes/test.yml

@@ -0,0 +1,39 @@
+- name: freebayes test_freebayes
+  command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: 04d60a7135768777e0c764daec6519db
+
+- name: freebayes test_freebayes_bed
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: fc6e228c8ac5508bd83da45eafc2e7b2
+
+- name: freebayes test_freebayes_cram
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: 91b8caaa0e396e1ba4f264a83bb67254
+
+- name: freebayes test_freebayes_somatic
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: 40da977199f16d9888e0e0e07e8bebee
+
+- name: freebayes test_freebayes_somatic_cram_intervals
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
+  tags:
+    - freebayes
+  files:
+    - path: output/freebayes/test.vcf.gz
+      md5sum: dd976880365287d9ad31a606eb4d091f