Add bracken (#1423)

* feat: add template for Bracken

* chore: update version

* refactor: change command build

* refactor: rename report variable, change quotes

* docs: remove refactored input parameter

* fix: correctly assign arguments to options

* tests: set up single and paired end tests

* style: apply prettier

* chore: change data sources to official ones

* refactor: rename test workflows

* tests: use correct input to the new UNTAR module

* chore: update md5sums

modules/bracken/bracken/main.nf

@@ -0,0 +1,41 @@
+process BRACKEN_BRACKEN {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bracken=2.6.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bracken:2.6.2--py39hc16433a_0':
+        'quay.io/biocontainers/bracken:2.6.2--py39hc16433a_0' }"
+
+    input:
+    tuple val(meta), path(kraken_report)
+    path database
+
+    output:
+    tuple val(meta), path(bracken_report), emit: reports
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def threshold = meta.threshold ?: 10
+    def taxonomic_level = meta.taxonomic_level ?: 'S'
+    def read_length = meta.read_length ?: 150
+    def args = task.ext.args ?: "-l ${taxonomic_level} -t ${threshold} -r ${read_length}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def bracken_version = '2.6.2'
+    bracken_report = "${prefix}_${taxonomic_level}.tsv"
+    """
+    bracken \\
+        ${args} \\
+        -d '${database}' \\
+        -i '${kraken_report}' \\
+        -o '${bracken_report}'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bracken: ${bracken_version}
+    END_VERSIONS
+    """
+}

modules/bracken/bracken/meta.yml

@@ -0,0 +1,45 @@
+name: bracken_bracken
+description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
+keywords:
+  - sort
+tools:
+  - bracken:
+      description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
+      homepage: https://ccb.jhu.edu/software/bracken/
+      documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
+      tool_dev_url: https://github.com/jenniferlu717/Bracken
+      doi: "10.7717/peerj-cs.104"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - kraken_report:
+      type: file
+      description: TSV file with six columns coming from kraken2 output
+      pattern: "*.{tsv}"
+  - database:
+      type: file
+      description: Directory containing the kraken2/Bracken files for analysis
+      pattern: "*"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reports:
+      type: file
+      description: TSV output report of the re-estimated abundances
+      pattern: "*.{tsv}"
+
+authors:
+  - "@Midnighter"

tests/config/pytest_modules.yml

@@ -313,6 +313,10 @@ bowtie2/build:
   - modules/bowtie2/build/**
   - tests/modules/bowtie2/build_test/**
 
+bracken/bracken:
+  - modules/bracken/bracken/**
+  - tests/modules/bracken/bracken/**
+
 bwa/aln:
   - modules/bwa/aln/**
   - tests/modules/bwa/aln/**

tests/config/test_data.config

@@ -25,6 +25,9 @@ params {
                 kraken2                                        = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
                 kraken2_tar_gz                                 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
 
+                kraken2_bracken                                = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2_bracken"
+                kraken2_bracken_tar_gz                         = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz"
+
                 ncbi_taxmap_zip                                = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip"
                 taxon_list_txt                                 = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/taxon_list.txt"
 

tests/modules/bracken/bracken/main.nf

@@ -0,0 +1,57 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR           } from '../../../../modules/untar/main.nf'
+include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
+include { BRACKEN_BRACKEN } from '../../../../modules/bracken/bracken/main.nf'
+
+workflow test_bracken_bracken_single_end_default_args {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+}
+
+workflow test_bracken_bracken_single_end_custom_args {
+    input = [ [ id:'test', single_end:true, threshold:0, taxonomic_level:'G', read_length:100 ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+}
+
+workflow test_bracken_bracken_paired_end_default_args {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+}
+
+workflow test_bracken_bracken_paired_end_custom_args {
+    input = [ [ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+}

tests/modules/bracken/bracken/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/bracken/bracken/test.yml

@@ -0,0 +1,43 @@
+- name: bracken bracken test_bracken_bracken_single_end_default_args
+  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_single_end_default_args -c tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_S.tsv
+      md5sum: 4a21ae14ff8a0311d55f139af5247838
+    - path: output/bracken/versions.yml
+      md5sum: ab8b1550f84a99bae80f050fe718abd0
+
+- name: bracken bracken test_bracken_bracken_single_end_custom_args
+  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_single_end_custom_args -c tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_G.tsv
+      md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
+    - path: output/bracken/versions.yml
+      md5sum: af87e8d4c42fbcb0469ab13912b8a9bd
+
+- name: bracken bracken test_bracken_bracken_paired_end_default_args
+  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_default_args -c tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_S.tsv
+      md5sum: 4a21ae14ff8a0311d55f139af5247838
+    - path: output/bracken/versions.yml
+      md5sum: 4602111eb25bd19a7f9d725acc5921f6
+
+- name: bracken bracken test_bracken_bracken_paired_end_custom_args
+  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_custom_args -c tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_G.tsv
+      md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
+    - path: output/bracken/versions.yml
+      md5sum: d4618b01df5ac09cc366fe2ae7c13f06