Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module

.github/workflows/ci.yml

@@ -23,6 +23,7 @@ jobs:
           - "21.10.3"
           - "latest-everything"
         parameters:
+          - "--preprocessing_qc_tool falco"
           - "--perform_longread_qc false"
           - "--perform_shortread_qc false"
           - "--shortread_qc_tool fastp"

CITATIONS.md

@@ -36,6 +36,10 @@
 
   > Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.
 
+- [Bracken](https://doi.org/10.7717/peerj-cs.104)
+
+  > Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: Estimating species abundance in metagenomics data. PeerJ Computer Science, 3, e104. doi: 10.7717/peerj-cs.104
+
 - [Krona](https://doi.org/10.1186/1471-2105-12-385)
 
   > Ondov, Brian D., Nicholas H. Bergman, and Adam M. Phillippy. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12 (1): 385. doi: 10.1186/1471-2105-12-385.
@@ -62,6 +66,10 @@
 
 - [FILTLONG](https://github.com/rrwick/Filtlong)
 
+- [falco](https://doi.org/10.12688/f1000research.21142.2)
+
+> de Sena Brandine G and Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research 2021, 8:1874
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

README.md

@@ -30,7 +30,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ![](docs/images/taxprofiler_tube.png)
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or [`falco`](https://github.com/smithlabcode/falco) as an alternative option)
 2. Performs optional read pre-processing
    - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop))
    - Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong))

assets/multiqc_config.yml

@@ -21,6 +21,7 @@ run_modules:
   - adapterRemoval
   - fastp
   - bowtie2
+  - samtools
   - kraken
   - malt
   - custom_content

conf/modules.config

@@ -40,6 +40,24 @@ process {
         ]
     }
 
+    withName: FALCO {
+        ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
+        publishDir = [
+            path: { "${params.outdir}/falco/raw" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{html,txt}'
+        ]
+    }
+
+    withName: FALCO_PROCESSED {
+        ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
+        publishDir = [
+            path: { "${params.outdir}/falco/processed" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{html,txt}'
+        ]
+    }
+
     withName: FASTP_SINGLE {
         ext.args   = [
             // trimming options
@@ -215,6 +233,16 @@ process {
         ]
     }
 
+    withName: SAMTOOLS_STATS {
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/samtools/stats" },
+            mode: params.publish_dir_mode,
+            enabled: params.save_hostremoval_unmapped,
+            pattern: '*stats'
+        ]
+    }
+
     withName: BBMAP_BBDUK {
         ext.args =  [
                 "entropy=${params.shortread_complexityfilter_entropy}",
@@ -277,7 +305,7 @@ process {
     }
 
     withName: KRAKEN2_KRAKEN2 {
-        ext.args = { "${meta.db_params}" }
+        ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}/" },
@@ -286,6 +314,16 @@ process {
         ]
     }
 
+    withName: BRACKEN_BRACKEN {
+        errorStrategy = 'ignore'
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/bracken/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.tsv'
+        ]
+    }
+
     withName: KRAKENTOOLS_COMBINEKREPORTS {
         ext.prefix = { "kraken2_${meta.id}_combined_reports" }
         publishDir = [

conf/test.config

@@ -34,6 +34,7 @@ params {
     hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
     run_kaiju                             = true
     run_kraken2                           = true
+    run_bracken                           = true
     run_malt                              = true
     run_metaphlan3                        = true
     run_centrifuge                        = true

conf/test_motus.config

@@ -33,6 +33,7 @@ params {
     hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
     run_kaiju                             = false
     run_kraken2                           = false
+    run_bracken                           = false
     run_malt                              = false
     run_metaphlan3                        = false
     run_centrifuge                        = false

conf/test_nopreprocessing.config

@@ -33,6 +33,7 @@ params {
     hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
     run_kaiju                             = true
     run_kraken2                           = true
+    run_bracken                           = true
     run_malt                              = true
     run_metaphlan3                        = true
     run_centrifuge                        = true

conf/test_noprofiling.config

@@ -34,6 +34,7 @@ params {
     hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
     run_kaiju                             = false
     run_kraken2                           = false
+    run_bracken                           = false
     run_malt                              = false
     run_metaphlan3                        = false
     run_centrifuge                        = false

conf/test_nothing.config

@@ -33,6 +33,7 @@ params {
     hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
     run_kaiju                             = false
     run_kraken2                           = false
+    run_bracken                           = false
     run_malt                              = false
     run_metaphlan3                        = false
     run_centrifuge                        = false

conf/test_pep.config

@@ -19,6 +19,7 @@ params {
     hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
     run_kaiju                             = true
     run_kraken2                           = true
+    run_bracken                           = true
     run_malt                              = true
     run_metaphlan3                        = true
     run_centrifuge                        = true

docs/usage.md

@@ -74,13 +74,13 @@ The pipeline takes the locations and specific profiling parameters of the tool o
 
 > ⚠️ nf-core/taxprofiler does not provide any databases by default, nor does it currently generate them for you. This must be performed manually by the user. See below for more information of the expected database files.
 
-An example database sheet can look as follows, where 4 tools are being used, and `malt` and `kraken2` will be used against two databases each.
+An example database sheet can look as follows, where 4 tools are being used, and `malt` and `kraken2` will be used against two databases each. This is because specifying `bracken` implies first running `kraken2` on the same database.
 
 ```console
 tool,db_name,db_params,db_path
 malt,malt85,-id 85,/<path>/<to>/malt/testdb-malt/
 malt,malt95,-id 90,/<path>/<to>/malt/testdb-malt.tar.gz
-kraken2,db1,,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
+bracken,db1,,/<path>/<to>/bracken/testdb-bracken.tar.gz
 kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
 centrifuge,db1,,/<path>/<to>/centrifuge/minigut_cf.tar.gz
 metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
@@ -91,8 +91,8 @@ Column specifications are as follows:
 
 | Column      | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
 | ----------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `tool`      | Taxonomic profiling tool (supported by nf-core/taxprofiler) that the database has been indexed for [required].                                                                                                                                                                                                                                                                                                                                                 |
+| `tool`      | Taxonomic profiling tool (supported by nf-core/taxprofiler) that the database has been indexed for [required]. Please note that `bracken` also implies running `kraken2` on the same database.                                                                                                                                                                                                                                                                 |
-| `db_name`   | A unique name of the particular database [required].                                                                                                                                                                                                                                                                                                                                                                                                           |
+| `db_name`   | A unique name per tool for the particular database [required]. Please note that names need to be unique across both `kraken2` and `bracken` as well, even if re-using the same database.                                                                                                                                                                                                                                                                       |
 | `db_params` | Any parameters of the given taxonomic profiler that you wish to specify that the taxonomic profiling tool should use when profiling against this specific. Can be empty to use taxonomic profiler defaults. Must not be surrounded by quotes [required]. We generally do not recommend specifying parameters here that turn on/off saving of output files or specifying particular file extensions - this should be already addressed via pipeline parameters. |
 | `db_path`   | Path to the database. Can either be a path to a directory containing the database index files or a `.tar.gz` file which contains the compressed database directory with the same name as the tar archive, minus `.tar.gz` [required].                                                                                                                                                                                                                          |
 
@@ -116,6 +116,15 @@ Expected (uncompressed) database files for each tool are as follows:
   - `opts.k2d`
   - `hash.k2d`
   - `taxo.k2d`
+- **Bracken** output of a combined `kraken2-` and `bracken-build` process. Please see the [documentation on Bracken](https://github.com/jenniferlu717/Bracken#running-bracken-easy-version) for details. The output is a directory containing files per expected sequencing read length similarly to:
+  - `hash.k2d`
+  - `opts.k2d`
+  - `taxo.k2d`
+  - `database.kraken`
+  - `database100mers.kmer_distrib`
+  - `database100mers.kraken`
+  - `database150mers.kmer_distrib`
+  - `database150mers.kraken`
 - **Centrifuge** output of `centrifuge-build`. A directory containing:
   - `<database_name>.<number>.cf`
   - `<database_name>.<number>.cf`
@@ -166,6 +175,10 @@ work                # Directory containing the nextflow working files
 # Other nextflow hidden files, eg. history of pipeline runs and old logs.
 ```
 
+### Sequencing quality control
+
+nf-core taxprofiler offers [`falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
+
 ### Preprocessing Steps
 
 nf-core/taxprofiler offers four main preprocessing steps
@@ -179,7 +192,7 @@ nf-core/taxprofiler offers four main preprocessing steps
 
 Raw sequencing read processing in the form of adapter clipping and paired-end read merging can be activated via the `--perform_shortread_qc` or `--perform_longread_qc` flags.
 
-It is highly recommended to run this on raw reads to remove artefacts from sequencing that can cause false positive identification of taxa (e.g. contaminated reference genomes) and/or skews in taxonomic abundance profiles.
+It is highly recommended to run this on raw reads to remove artifacts from sequencing that can cause false positive identification of taxa (e.g. contaminated reference genomes) and/or skews in taxonomic abundance profiles.
 
 There are currently two options for short-read preprocessing: `fastp` or `adapterremoval`.
 

modules.json

@@ -21,6 +21,10 @@
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
+                    "bracken/bracken": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
                     "cat/fastq": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
@@ -49,6 +53,10 @@
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
+                    "falco": {
+                        "branch": "master",
+                        "git_sha": "fc959214036403ad83efe7a41d43d0606c445cda"
+                    },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
@@ -149,6 +157,14 @@
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/stats": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"

modules/local/kraken2_standard_report.nf

@@ -0,0 +1,32 @@
+process KRAKEN2_STANDARD_REPORT {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? 'conda-forge::sed=4.8' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
+        'biocontainers/biocontainers:v1.2.0_cv2' }"
+
+    input:
+    tuple val(meta), path(report)
+
+    output:
+    tuple val(meta), path(result), emit: report
+    path 'versions.yml'          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    result = "${prefix}_standardized.kraken2.report.txt"
+    """
+    cut -f1-3,6-8 '${report}' > '${result}'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cut: \$(echo \$(cut --version 2>&1) | sed 's/^.*(GNU coreutils) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+}
+

modules/nf-core/bracken/bracken/main.nf

@@ -0,0 +1,45 @@
+process BRACKEN_BRACKEN {
+    tag "$meta.id"
+    label 'process_low'
+
+    // WARN: Version information not provided by tool on CLI.
+    // Please update version string below when bumping container versions.
+    conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
+    container "${ 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:
+    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}"
+    bracken_report = "${prefix}_${taxonomic_level}.tsv"
+    // WARN: Version information not provided by tool on CLI.
+    // Please update version string below when bumping container versions.
+    def VERSION = '2.7'
+    """
+    bracken \\
+        ${args} \\
+        -d '${database}' \\
+        -i '${kraken_report}' \\
+        -o '${bracken_report}'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bracken: ${VERSION}
+    END_VERSIONS
+    """
+}

modules/nf-core/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"

modules/nf-core/falco/main.nf

@@ -0,0 +1,57 @@
+process FALCO {
+    tag "$meta.id"
+    label 'process_single'
+
+
+    conda (params.enable_conda ? "bioconda::falco=1.2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3':
+        'quay.io/biocontainers/falco:1.2.1--h867801b_3' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), 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 ?: "${meta.id}"
+    if ( reads.toList().size() == 1 ) {
+        """
+        falco $args --threads $task.cpus ${reads} -D ${prefix}_data.txt -S ${prefix}_summary.txt -R ${prefix}_report.html
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            falco:\$( falco --version | sed -e "s/falco//g" )
+        END_VERSIONS
+        """
+    } else {
+        """
+        falco $args --threads $task.cpus ${reads}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            falco:\$( falco --version | sed -e "s/falco//g" )
+        END_VERSIONS
+        """
+    }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_data.txt
+    touch ${prefix}_fastqc_data.html
+    touch ${prefix}_summary.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        falco: \$( falco --version | sed -e "s/falco v//g" )
+    END_VERSIONS
+    """
+}

modules/nf-core/falco/meta.yml

@@ -0,0 +1,52 @@
+name: falco
+description: Run falco on sequenced reads
+keywords:
+  - quality control
+  - qc
+  - adapters
+  - fastq
+tools:
+  - fastqc:
+      description: "falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads."
+
+      homepage: "https://falco.readthedocs.io/"
+      documentation: "https://falco.readthedocs.io/"
+      tool_dev_url: "None"
+      doi: ""
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - html:
+      type: file
+      description: FastQC like report
+      pattern: "*_{fastqc_report.html}"
+  - txt:
+      type: file
+      description: falco report data
+      pattern: "*_{data.txt}"
+  - txt:
+      type: file
+      description: falco summary file
+      pattern: "*_{summary.txt}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@lucacozzuto"

modules/nf-core/samtools/index/main.nf

@@ -0,0 +1,48 @@
+process SAMTOOLS_INDEX {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("*.bai") , optional:true, emit: bai
+    tuple val(meta), path("*.csi") , optional:true, emit: csi
+    tuple val(meta), path("*.crai"), optional:true, emit: crai
+    path  "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    samtools \\
+        index \\
+        -@ ${task.cpus-1} \\
+        $args \\
+        $input
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${input}.bai
+    touch ${input}.crai
+    touch ${input}.csi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}

modules/nf-core/samtools/index/meta.yml

@@ -0,0 +1,53 @@
+name: samtools_index
+description: Index SAM/BAM/CRAM file
+keywords:
+  - index
+  - bam
+  - sam
+  - cram
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: hhttp://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bai:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai,sai}"
+  - crai:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai,sai}"
+  - csi:
+      type: file
+      description: CSI index file
+      pattern: "*.{csi}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@ewels"
+  - "@maxulysse"

modules/nf-core/samtools/stats/main.nf

@@ -0,0 +1,49 @@
+process SAMTOOLS_STATS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+
+    input:
+    tuple val(meta), path(input), path(input_index)
+    path fasta
+
+    output:
+    tuple val(meta), path("*.stats"), emit: stats
+    path  "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def reference = fasta ? "--reference ${fasta}" : ""
+    """
+    samtools \\
+        stats \\
+        --threads ${task.cpus} \\
+        ${reference} \\
+        ${input} \\
+        > ${prefix}.stats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.stats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}

modules/nf-core/samtools/stats/meta.yml

@@ -0,0 +1,53 @@
+name: samtools_stats
+description: Produces comprehensive statistics from SAM/BAM/CRAM file
+keywords:
+  - statistics
+  - counts
+  - bam
+  - sam
+  - cram
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: hhttp://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      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 file from alignment
+    pattern: "*.{bam,cram}"
+  - input_index:
+    type: file
+    description: BAI/CRAI file from alignment
+    pattern: "*.{bai,crai}"
+  - fasta:
+      type: optional file
+      description: Reference file the CRAM was created with
+      pattern: "*.{fasta,fa}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - stats:
+      type: file
+      description: File containing samtools stats output
+      pattern: "*.{stats}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@FriederikeHanssen"

nextflow.config

@@ -59,6 +59,8 @@ params {
     // Databases
     databases = null
 
+    preprocessing_qc_tool            = 'fastqc'
+
     // FASTQ preprocessing
     perform_shortread_qc             = false
     shortread_qc_tool                = 'fastp'
@@ -114,6 +116,10 @@ params {
     run_kraken2                     = false
     kraken2_save_reads              = false // added directly to module in profiling.nf
     kraken2_save_readclassification = false // added directly to module in profiling.nf
+    kraken2_save_minimizers         = false
+
+    // Bracken
+    run_bracken = false
 
     // centrifuge
     run_centrifuge             = false

nextflow_schema.json

@@ -10,7 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir", "databases"],
+            "required": ["input", "databases", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -382,6 +382,17 @@
                     "description": "Turn on saving of Kraken2 per-read taxonomic assignment file",
                     "help_text": "Save a text file that contains a list of each read that had a taxonomic assignment, with information on specific taxonomic taxonomic assignment that that read recieved.\n\n> Modifies tool parameter(s):\n> - kraken2: `--output`"
                 },
+                "kraken2_save_minimizers": {
+                    "type": "boolean",
+                    "description": "Turn on saving minimizer information in the kraken2 report thus increasing to an eight column layout.",
+                    "fa_icon": "fas fa-save",
+                    "help_text": "Turn on saving minimizer information in the kraken2 report thus increasing to an eight column layout.\n\nAdds `--report-minimizer-data` to the kraken2 command."
+                },
+                "run_bracken": {
+                    "type": "boolean",
+                    "description": "Post-process kraken2 reports with Bracken.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
                 "run_malt": {
                     "type": "boolean",
                     "fa_icon": "fas fa-toggle-on",
@@ -707,5 +718,14 @@
         {
             "$ref": "#/definitions/reference_genome_options"
         }
-    ]
+    ],
+    "properties": {
+        "preprocessing_qc_tool": {
+            "type": "string",
+            "default": "fastqc",
+            "enum": ["fastqc", "falco"],
+            "help_text": "Falco is designed as a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
+            "description": "Specify the tool used for quality control of raw sequencing reads"
+        }
+    }
 }

subworkflows/local/longread_hostremoval.nf

@@ -6,6 +6,8 @@ include { MINIMAP2_INDEX             } from '../../modules/nf-core/minimap2/inde
 include { MINIMAP2_ALIGN             } from '../../modules/nf-core/minimap2/align/main'
 include { SAMTOOLS_VIEW              } from '../../modules/nf-core/samtools/view/main'
 include { SAMTOOLS_BAM2FQ            } from '../../modules/nf-core/samtools/bam2fq/main'
+include { SAMTOOLS_INDEX             } from '../../modules/nf-core/samtools/index/main'
+include { SAMTOOLS_STATS             } from '../../modules/nf-core/samtools/stats/main'
 
 workflow LONGREAD_HOSTREMOVAL {
     take:
@@ -39,9 +41,21 @@ workflow LONGREAD_HOSTREMOVAL {
     SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )
     ch_versions      = ch_versions.mix( SAMTOOLS_BAM2FQ.out.versions.first() )
 
+    SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
+    ch_versions      = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
+
+    bam_bai = SAMTOOLS_VIEW.out.bam
+        .join(SAMTOOLS_INDEX.out.bai, remainder: true)
+
+    SAMTOOLS_STATS ( bam_bai, reference )
+    ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
+    ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats )
+
 
     emit:
+    stats    = SAMTOOLS_STATS.out.stats     //channel: [val(meta), [reads  ] ]
     reads    = SAMTOOLS_BAM2FQ.out.reads   // channel: [ val(meta), [ reads ] ]
     versions = ch_versions                 // channel: [ versions.yml ]
+    mqc      = ch_multiqc_files
 }
 

subworkflows/local/longread_preprocessing.nf

@@ -3,6 +3,8 @@
 //
 
 include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
+include { FALCO as FALCO_PROCESSED   } from '../../modules/nf-core/falco/main'
+
 include { PORECHOP                   } from '../../modules/nf-core/porechop/main'
 include { FILTLONG                   } from '../../modules/nf-core/filtlong/main'
 
@@ -52,9 +54,17 @@ workflow LONGREAD_PREPROCESSING {
         ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
     }
 
+    if (params.preprocessing_qc_tool == 'fastqc') {
         FASTQC_PROCESSED ( ch_processed_reads )
+        ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
         ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
 
+    } else if (params.preprocessing_qc_tool == 'falco') {
+        FALCO_PROCESSED ( ch_processed_reads )
+        ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions )
+        ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
+    }
+
     emit:
     reads    = ch_processed_reads   // channel: [ val(meta), [ reads ] ]
     versions = ch_versions          // channel: [ versions.yml ]

subworkflows/local/profiling.nf

@@ -5,6 +5,8 @@
 include { MALT_RUN                              } from '../../modules/nf-core/malt/run/main'
 include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV  } from '../../modules/nf-core/megan/rma2info/main'
 include { KRAKEN2_KRAKEN2                       } from '../../modules/nf-core/kraken2/kraken2/main'
+include { KRAKEN2_STANDARD_REPORT                } from '../../modules/local/kraken2_standard_report'
+include { BRACKEN_BRACKEN                       } from '../../modules/nf-core/bracken/bracken/main'
 include { CENTRIFUGE_CENTRIFUGE                 } from '../../modules/nf-core/centrifuge/centrifuge/main'
 include { CENTRIFUGE_KREPORT                    } from '../../modules/nf-core/centrifuge/kreport/main'
 include { METAPHLAN3_METAPHLAN3                 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
@@ -40,7 +42,7 @@ workflow PROFILING {
             .combine(databases)
             .branch {
                 malt:    it[2]['tool'] == 'malt'
-                kraken2: it[2]['tool'] == 'kraken2'
+                kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
                 metaphlan3: it[2]['tool'] == 'metaphlan3'
                 centrifuge: it[2]['tool'] == 'centrifuge'
                 kaiju: it[2]['tool'] == 'kaiju'
@@ -131,7 +133,42 @@ workflow PROFILING {
         ch_multiqc_files       = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report )
         ch_versions            = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
-        ch_raw_profiles        = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
+        ch_raw_profiles        = ch_raw_profiles.mix(
+            KRAKEN2_KRAKEN2.out.report
+                // Set the tool to be strictly 'kraken2' instead of potentially 'bracken' for downstream use.
+                // Will remain distinct from 'pure' Kraken2 results due to distinct database names in file names.
+                .map { meta, report -> [meta + [tool: 'kraken2'], report]}
+        )
+
+    }
+
+    if ( params.run_kraken2 && params.run_bracken ) {
+        // Remove files from 'pure' kraken2 runs, so only those aligned against Bracken & kraken2 database are used.
+        def ch_kraken2_output = KRAKEN2_KRAKEN2.out.report
+            .filter { meta, report -> meta['tool'] == 'bracken' }
+
+        // If necessary, convert the eight column output to six column output.
+        if (params.kraken2_save_minimizers) {
+            ch_kraken2_output = KRAKEN2_STANDARD_REPORT(ch_kraken2_output).report
+        }
+
+        // Extract the database name to combine by.
+        ch_bracken_databases = databases
+            .filter { meta, db -> meta['tool'] == 'bracken' }
+            .map { meta, db -> [meta['db_name'], meta, db] }
+
+        // Extract the database name to combine by.
+        ch_input_for_bracken = ch_kraken2_output
+            .map { meta, report -> [meta['db_name'], meta, report] }
+            .combine(ch_bracken_databases, by: 0)
+            .multiMap { key, meta, report, db_meta, db ->
+                report: [meta + db_meta, report]
+                db: db
+            }
+
+        BRACKEN_BRACKEN(ch_input_for_bracken.report, ch_input_for_bracken.db)
+        ch_versions     = ch_versions.mix(BRACKEN_BRACKEN.out.versions.first())
+        ch_raw_profiles = ch_raw_profiles.mix(BRACKEN_BRACKEN.out.reports)
 
     }
 

subworkflows/local/shortread_preprocessing.nf

@@ -6,6 +6,7 @@
 include { SHORTREAD_FASTP             } from './shortread_fastp'
 include { SHORTREAD_ADAPTERREMOVAL    } from './shortread_adapterremoval'
 include { FASTQC as FASTQC_PROCESSED  } from '../../modules/nf-core/fastqc/main'
+include { FALCO as FALCO_PROCESSED    } from '../../modules/nf-core/falco/main'
 
 workflow SHORTREAD_PREPROCESSING {
     take:
@@ -27,9 +28,15 @@ workflow SHORTREAD_PREPROCESSING {
         ch_processed_reads = reads
     }
 
+    if (params.preprocessing_qc_tool == 'fastqc') {
         FASTQC_PROCESSED ( ch_processed_reads )
         ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
         ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
+    } else if  (params.preprocessing_qc_tool == 'falco') {
+        FALCO_PROCESSED ( ch_processed_reads )
+        ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions )
+        ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
+    }
 
     emit:
     reads    = ch_processed_reads   // channel: [ val(meta), [ reads ] ]

workflows/taxprofiler.nf

@@ -41,6 +41,7 @@ if (params.longread_hostremoval_index      ) { ch_longread_reference_index  = fi
 if (params.diamond_save_reads              ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available."
 
 if (params.run_malt && params.run_krona && !params.krona_taxonomy_directory) log.warn "[nf-core/taxprofiler] Krona can only be run on MALT output if path to Krona taxonomy database supplied to --krona_taxonomy_directory. Krona will not be executed in this run for MALT."
+if (params.run_bracken && !params.run_kraken2) exit 1, 'ERROR: [nf-core/taxprofiler] You are attempting to run Bracken without running kraken2. This is not possible! Please set --run_kraken2 as well.'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -84,6 +85,7 @@ include { STANDARDISATION_PROFILES      } from '../subworkflows/local/standardis
 // MODULE: Installed directly from nf-core/modules
 //
 include { FASTQC                      } from '../modules/nf-core/fastqc/main'
+include { FALCO                       } from '../modules/nf-core/falco/main'
 include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 include { CAT_FASTQ                   } from '../modules/nf-core/cat/fastq/main'
@@ -120,12 +122,13 @@ workflow TAXPROFILER {
     */
     ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
 
-    FASTQC (
+    if ( params.preprocessing_qc_tool == 'falco' ) {
-        ch_input_for_fastqc
+        FALCO ( ch_input_for_fastqc )
-    )
+        ch_versions = ch_versions.mix(FALCO.out.versions.first())
-
+    } else {
+        FASTQC ( ch_input_for_fastqc )
         ch_versions = ch_versions.mix(FASTQC.out.versions.first())
-
+    }
     /*
         SUBWORKFLOW: PERFORM PREPROCESSING
     */
@@ -254,7 +257,13 @@ workflow TAXPROFILER {
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
+
+    if ( params.preprocessing_qc_tool == 'falco' ) {
+        ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect{it[1]}.ifEmpty([]))
+    } else {
         ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+    }
+
 
     if (params.perform_shortread_qc) {
         ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
@@ -272,6 +281,10 @@ workflow TAXPROFILER {
         ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
     }
 
+     if (params.perform_longread_hostremoval) {
+        ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
+    }
+
     ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc.collect{it[1]}.ifEmpty([]) )
 
     if ( params.run_profile_standardisation ) {