Add bracken/combinebrackenoutputs (#2022)

* Add combinebrackenoutputs

* Prettier and relax tests contains

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

modules/bracken/combinebrackenoutputs/main.nf

@@ -0,0 +1,36 @@
+process BRACKEN_COMBINEBRACKENOUTPUTS {
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
+        'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
+
+    input:
+    path input
+
+    output:
+    path "*.txt"       , emit: txt
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "bracken_combined.txt"
+    // WARN: Version information not provided by tool on CLI.
+    // Please update version string below when bumping container versions.
+    def VERSION = '2.7'
+    """
+    combine_bracken_outputs.py \\
+        $args \\
+        --files ${input} \\
+        -o ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        combine_bracken_output: ${VERSION}
+    END_VERSIONS
+    """
+}

modules/bracken/combinebrackenoutputs/meta.yml

@@ -0,0 +1,31 @@
+name: "bracken_combinebrackenoutputs"
+description: Combine output of metagenomic samples analyzed by bracken.
+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:
+  - input:
+      type: file
+      description: List of output files from bracken
+      pattern: "*"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - txt:
+      type: file
+      description: Combined output in table format
+      pattern: "*.txt"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -397,6 +397,10 @@ bracken/bracken:
   - modules/bracken/bracken/**
   - tests/modules/bracken/bracken/**
 
+bracken/combinebrackenoutputs:
+  - modules/bracken/combinebrackenoutputs/**
+  - tests/modules/bracken/combinebrackenoutputs/**
+
 busco:
   - modules/busco/**
   - tests/modules/busco/**

tests/modules/bracken/combinebrackenoutputs/main.nf

@@ -0,0 +1,25 @@
+#!/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'
+include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../../../modules/bracken/combinebrackenoutputs/main.nf'
+
+workflow test_bracken_combinebrackenoutputs {
+
+    input = Channel.of(
+        [[ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
+        [[ id:'test2', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ 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, false, false )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
+
+    BRACKEN_COMBINEBRACKENOUTPUTS ( BRACKEN_BRACKEN.out.reports.map{it[1]}.collect() )
+}
+

tests/modules/bracken/combinebrackenoutputs/nextflow.config

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

tests/modules/bracken/combinebrackenoutputs/test.yml

@@ -0,0 +1,9 @@
+- name: bracken combinebrackenoutputs test_bracken_combinebrackenoutputs
+  command: nextflow run ./tests/modules/bracken/combinebrackenoutputs -entry test_bracken_combinebrackenoutputs -c ./tests/config/nextflow.config  -c ./tests/modules/bracken/combinebrackenoutputs/nextflow.config
+  tags:
+    - bracken/combinebrackenoutputs
+    - bracken
+  files:
+    - path: output/bracken/bracken_combined.txt
+      contains:
+        - "name	taxonomy_id	taxonomy_lvl"