Start work on host removal

modules.json

@@ -6,6 +6,12 @@
             "adapterremoval": {
                 "git_sha": "f0800157544a82ae222931764483331a81812012"
             },
+            "bowtie2/align": {
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            },
+            "bowtie2/build": {
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            },
             "cat/fastq": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
@@ -30,6 +36,9 @@
             "porechop": {
                 "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
+            "samtools/flagstat": {
+                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
+            },
             "untar": {
                 "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
             }

modules/nf-core/modules/bowtie2/align/main.nf

@@ -0,0 +1,77 @@
+process BOWTIE2_ALIGN {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
+        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+    val   save_unaligned
+
+    output:
+    tuple val(meta), path('*.bam')    , emit: bam
+    tuple val(meta), path('*.log')    , emit: log
+    tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
+    path  "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.single_end) {
+        def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
+        """
+        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        bowtie2 \\
+            -x \$INDEX \\
+            -U $reads \\
+            --threads $task.cpus \\
+            $unaligned \\
+            $args \\
+            2> ${prefix}.bowtie2.log \\
+            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+        END_VERSIONS
+        """
+    } else {
+        def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
+        """
+        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        bowtie2 \\
+            -x \$INDEX \\
+            -1 ${reads[0]} \\
+            -2 ${reads[1]} \\
+            --threads $task.cpus \\
+            $unaligned \\
+            $args \\
+            2> ${prefix}.bowtie2.log \\
+            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
+
+        if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
+            mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
+        fi
+        if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
+            mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
+        fi
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+        END_VERSIONS
+        """
+    }
+}

modules/nf-core/modules/bowtie2/align/meta.yml

@@ -0,0 +1,51 @@
+name: bowtie2_align
+description: Align reads to a reference genome using bowtie2
+keywords:
+  - align
+  - fasta
+  - genome
+  - reference
+tools:
+  - bowtie2:
+      description: |
+        Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+        sequencing reads to long reference sequences.
+      homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+      documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
+      doi: 10.1038/nmeth.1923
+      licence: ["GPL-3.0-or-later"]
+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.
+  - index:
+      type: file
+      description: Bowtie2 genome index files
+      pattern: "*.ebwt"
+output:
+  - bam:
+      type: file
+      description: Output BAM file containing read alignments
+      pattern: "*.{bam}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - fastq:
+      type: file
+      description: Unaligned FastQ files
+      pattern: "*.fastq.gz"
+  - log:
+      type: file
+      description: Aligment log
+      pattern: "*.log"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"

modules/nf-core/modules/bowtie2/build/main.nf

@@ -0,0 +1,30 @@
+process BOWTIE2_BUILD {
+    tag "$fasta"
+    label 'process_high'
+
+    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
+        'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
+
+    input:
+    path fasta
+
+    output:
+    path 'bowtie2'      , emit: index
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    mkdir bowtie2
+    bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/nf-core/modules/bowtie2/build/meta.yml

@@ -0,0 +1,33 @@
+name: bowtie2_build
+description: Builds bowtie index for reference genome
+keywords:
+  - build
+  - index
+  - fasta
+  - genome
+  - reference
+tools:
+  - bowtie2:
+      description: |
+        Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+        sequencing reads to long reference sequences.
+      homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+      documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
+      doi: 10.1038/nmeth.1923
+      licence: ["GPL-3.0-or-later"]
+input:
+  - fasta:
+      type: file
+      description: Input genome fasta file
+output:
+  - index:
+      type: file
+      description: Bowtie2 genome index files
+      pattern: "*.bt2"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"

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

@@ -0,0 +1,34 @@
+process SAMTOOLS_FLAGSTAT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+
+    output:
+    tuple val(meta), path("*.flagstat"), emit: flagstat
+    path  "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    samtools \\
+        flagstat \\
+        --threads ${task.cpus-1} \\
+        $bam \\
+        > ${bam}.flagstat
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,49 @@
+name: samtools_flagstat
+description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
+keywords:
+  - stats
+  - mapping
+  - 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 ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - bai:
+      type: file
+      description: Index for BAM/CRAM/SAM file
+      pattern: "*.{bai,crai,sai}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - flagstat:
+      type: file
+      description: File containing samtools flagstat output
+      pattern: "*.{flagstat}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"

nextflow.config

@@ -65,6 +65,10 @@ params {
     shortread_clipmerge_minlength           = 15
     longread_clip                           = false
 
+    // Host Removal
+    shortread_hostremoval_reference = null
+    shortread_hostremoval_index     = null
+
     // MALT
     run_malt                   = false
     malt_mode                  = 'BlastN'

subworkflows/local/shortread_hostremoval.nf

@@ -0,0 +1,39 @@
+//
+// Remove host reads via alignment and export off-target reads
+//
+
+include { BOWTIE2_ALIGN             } from '../../../modules/nf-core/modules/bowtie2/align/main'
+include { BOWTIE2_BUILD             } from '../../../modules/nf-core/modules/bowtie2/build/main'
+include { SAMTOOLS_VIEW             } from '../../../modules/nf-core/modules/samtools/view/main'
+include { SAMTOOLS_FASTQ            } from '../../../modules/nf-core/modules/samtools/fastq/main'
+include { SAMTOOLS_FLAGSTAT         } from '../../../modules/nf-core/modules/samtools/flagstat/main'
+
+workflow SHORTREAD_PREPROCESSING {
+    take:
+    reads     // [ [ meta ], [ reads ] ]
+    reference // /path/to/fasta
+
+    main:
+    ch_versions       = Channel.empty()
+    ch_multiqc_files  = Channel.empty()
+
+    if ( !params.shortread_hostremoval_index ) {
+        file( , checkIfExists: true )
+        BOWTIE2_BUILD ( reference )
+        ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
+    }
+
+    BOWTIE2_ALIGN ( reads, BOWTIE2_BUILD.out.index )
+    ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
+    ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_FLAGSTAT.out.log )
+
+    SAMTOOLS_FLAGSTAT ( BOWTIE2_ALIGN.out.bam )
+    ch_versions = ch_versions.mix( SAMTOOLS_FLAGSTAT.out.versions )
+    ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_FLAGSTAT.out.flagstat )
+
+    emit:
+    reads    = BOWTIE2_ALIGN.out.fastq   // channel: [ val(meta), [ reads ] ]
+    versions = ch_versions          // channel: [ versions.yml ]
+    mqc      = ch_multiqc_files
+}
+

workflows/taxprofiler.nf

@@ -11,7 +11,9 @@ WorkflowTaxprofiler.initialise(params, log)
 
 // TODO nf-core: Add all file path parameters for the pipeline to the list below
 // Check input path parameters to see if they exist
-def checkPathParamList = [ params.input, params.databases, params.multiqc_config ]
+def checkPathParamList = [ params.input, params.databases, params.shortread_hostremoval_reference,
+                            params.shortread_hostremoval_index, params.multiqc_config
+                        ]
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters
@@ -20,6 +22,10 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
 if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not except uncollapsed paired-reads. Pairs will be profiled as separate files."
 if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
 
+// TODO Add check if index but no reference exit 1
+if (params.shortread_hostremoval_reference   ) { ch_reference       = file(params.shortread_hostremoval_reference) } else {    }
+if (params.shortread_hostremoval_index)        { ch_reference_index = file(params.shortread_hostremoval_index    ) } else { ch_reference_index = [] }
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CONFIG FILES