Merge branch 'master' into gatk4-mergevcfs

.github/filters.yml

@@ -132,6 +132,14 @@ gatk4_mergevcfs:
   - software/gatk4/mergevcfs/**
   - tests/software/gatk4/mergevcfs/**
 
+gatk4_bedtointervallist:
+  - software/gatk4/bedtointervallist/**
+  - tests/software/gatk4/bedtointervallist/**
+
+gatk4_samtofastq:
+  - software/gatk4/samtofastq/**
+  - tests/software/gatk4/samtofastq/**
+
 gffread:
   - software/gffread/**
   - tests/software/gffread/**

software/gatk4/bedtointervallist/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/gatk4/bedtointervallist/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process GATK4_BEDTOINTERVALLIST {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
+    } else {
+        container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
+    }
+
+    input:
+    tuple val(meta), path(bed)
+    path sequence_dict
+
+    output:
+    tuple val(meta), path('*.interval_list'), emit: interval_list
+    path  '*.version.txt'                   , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+    """
+    gatk BedToIntervalList \\
+        -I $bed \\
+        -SD $sequence_dict \\
+        -O ${prefix}.interval_list \\
+        $options.args
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}

software/gatk4/bedtointervallist/meta.yml

@@ -0,0 +1,60 @@
+name: gatk4_bedtointervallist
+description: Creates an interval list from a bed file and a reference dict
+keywords:
+  - bed
+  - interval list
+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
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bed:
+      type: file
+      description: Input bed file
+      pattern: "*.bed"
+  - dict:
+      type: file
+      description: Sequence dictionary
+      pattern: "*.dict"
+output:
+  - interval_list:
+      type: file
+      description: gatk interval list file
+      pattern: "*.interval_list"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
+authors:
+  - "@kevinmenden"

software/gatk4/samtofastq/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/gatk4/samtofastq/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process GATK4_SAMTOFASTQ {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
+    } else {
+        container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
+    }
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path('*.fastq.gz')     , emit: fastq
+    path  '*.version.txt'                   , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+    def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz"
+    """
+    gatk SamToFastq \\
+        I=$bam \\
+        $output \\
+        $options.args
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}

software/gatk4/samtofastq/meta.yml

@@ -0,0 +1,56 @@
+name: gatk4_samtofastq
+description: Converts BAM/SAM file to FastQ format
+keywords:
+  - bed
+  - interval list
+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
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bam:
+      type: file
+      description: Input SAM/BAM file
+      pattern: "*.{bam,sam}"
+output:
+  - fastq:
+      type: file
+      description: converted fastq file
+      pattern: "*.fastq"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
+authors:
+  - "@kevinmenden"

tests/data/bed/sarscov2.bed

@@ -0,0 +1,4 @@
+MT192765.1	1242	1264	nCoV-2019_5_LEFT	1	+
+MT192765.1	1623	1651	nCoV-2019_5_RIGHT	1	-
+MT192765.1	1573	1595	nCoV-2019_6_LEFT	2	+
+MT192765.1	1942	1964	nCoV-2019_6_RIGHT	2	-

tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict

@@ -0,0 +1,2 @@
+@HD	VN:1.6
+@SQ	SN:MT192765.1	LN:29829	M5:c95f3e5592d0ad9974e41e7f0ea14eb0	UR:file:/Users/kevin/Documents/nfcore/modules/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna

tests/software/gatk4/bedtointervallist/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_BEDTOINTERVALLIST } from '../../../../software/gatk4/bedtointervallist/main.nf' addParams( options: [:] )
+
+workflow test_gatk4_bedtointervallist {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/bed/sarscov2.bed", checkIfExists: true)] ]
+
+    sd = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict", checkIfExists: true)
+
+    GATK4_BEDTOINTERVALLIST ( input, sd )
+}

tests/software/gatk4/bedtointervallist/test.yml

@@ -0,0 +1,8 @@
+- name: gatk4 bedtointervallist
+  command: nextflow run ./tests/software/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_bedtointervallist
+  files:
+    - path: output/gatk4/test.interval_list
+      md5sum: e51101c9357fb2d59fd30e370eefa39c

tests/software/gatk4/samtofastq/main.nf

@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_SAMTOFASTQ } from '../../../../software/gatk4/samtofastq/main.nf' addParams( options: [:] )
+
+workflow test_gatk4_samtofastq_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end: true ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.single_end.sorted.bam", checkIfExists: true)] ]
+
+    GATK4_SAMTOFASTQ ( input )
+}
+
+workflow test_gatk4_samtofastq_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end: false ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.single_end.sorted.bam", checkIfExists: true)] ]
+
+    GATK4_SAMTOFASTQ ( input )
+}

tests/software/gatk4/samtofastq/test.yml

@@ -0,0 +1,21 @@
+- name: gatk4 samtofastq single-end
+  command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_samtofastq
+    - gatk4_samtofastq_single_end
+  files:
+    - path: output/gatk4/test.fastq.gz
+      md5sum: 61c6d3556ac6e0d09d800415b9a48508
+
+- name: gatk4 samtofastq paired-end
+  command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_samtofastq
+    - gatk4_samtofastq_paired_end
+  files:
+    - path: output/gatk4/test_1.fastq.gz
+      md5sum: 61c6d3556ac6e0d09d800415b9a48508
+    - path: output/gatk4/test_2.fastq.gz
+      md5sum: d0e74ab8dccca91c0ccd7125e588d5cd