Remove flagstat as bowtie2 reports this itself

conf/modules.config

@@ -132,7 +132,6 @@ process {
         ]
     }
 
-
     withName: PORECHOP {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
@@ -142,6 +141,24 @@ process {
         ]
     }
 
+    withName: BOWTIE2_BUILD {
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/bowtie2/build" },
+            mode: 'copy',
+            pattern: '*.bt2'
+        ]
+    }
+
+    withName: BOWTIE2_ALIGN {
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/bowtie2/align" },
+            mode: 'copy',
+            pattern: '*.{fastq.gz,bam}'
+        ]
+    }
+
     withName: CAT_FASTQ {
         publishDir = [
             path: { "${params.outdir}/prepared_sequences" },

conf/test.config

@@ -22,10 +22,12 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
-    databases           = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
-    run_kraken2         = true
-    run_malt            = true
-    shortread_clipmerge = true
+    input                           = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    databases                       = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
+    run_kraken2                     = true
+    run_malt                        = true
+    shortread_clipmerge             = true
+    shortread_hostremoval           = true
+    shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
 
 }

modules.json

@@ -36,9 +36,6 @@
             "porechop": {
                 "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
-            "samtools/flagstat": {
-                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
-            },
             "untar": {
                 "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
             }

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

@@ -1,34 +0,0 @@
-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

@@ -1,49 +0,0 @@
-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

@@ -66,6 +66,7 @@ params {
     longread_clip                           = false
 
     // Host Removal
+    shortread_hostremoval           = false
     shortread_hostremoval_reference = null
     shortread_hostremoval_index     = null
 

nextflow_schema.json

@@ -266,8 +266,7 @@
             "type": "boolean"
         },
         "shortread_clipmerge_excludeunmerged": {
-            "type": "boolean",
-            "default": false
+            "type": "boolean"
         },
         "longread_clip": {
             "type": "boolean"
@@ -304,6 +303,17 @@
         "shortread_clipmerge_minlength": {
             "type": "integer",
             "default": 15
+        },
+        "shortread_hostremoval": {
+            "type": "boolean"
+        },
+        "shortread_hostremoval_reference": {
+            "type": "string",
+            "default": null
+        },
+        "shortread_hostremoval_index": {
+            "type": "string",
+            "default": null
         }
     }
 }

subworkflows/local/shortread_hostremoval.nf

@@ -2,38 +2,33 @@
 // 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'
+include { BOWTIE2_BUILD             } from '../../modules/nf-core/modules/bowtie2/build/main'
+include { BOWTIE2_ALIGN             } from '../../modules/nf-core/modules/bowtie2/align/main'
 
-workflow SHORTREAD_PREPROCESSING {
+workflow SHORTREAD_HOSTREMOVAL {
     take:
     reads     // [ [ meta ], [ reads ] ]
     reference // /path/to/fasta
+    index     // /path/to/index
 
     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 )
+        ch_bowtie2_index = BOWTIE2_BUILD ( reference ).index
+        ch_versions      = ch_versions.mix( BOWTIE2_BUILD.out.versions )
+    } else {
+        ch_bowtie2_index = index.first()
     }
 
-    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 )
+    BOWTIE2_ALIGN ( reads, ch_bowtie2_index, true )
+    ch_versions      = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() )
+    ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
 
     emit:
     reads    = BOWTIE2_ALIGN.out.fastq   // channel: [ val(meta), [ reads ] ]
-    versions = ch_versions          // channel: [ versions.yml ]
+    versions = ch_versions               // channel: [ versions.yml ]
     mqc      = ch_multiqc_files
 }
 

workflows/taxprofiler.nf

@@ -23,8 +23,11 @@ if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-cor
 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 = [] }
+if (params.shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
+if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
+
+if (params.shortread_hostremoval_reference ) { ch_reference       = file(params.shortread_hostremoval_reference) } else { ch_reference       = [] }
+if (params.shortread_hostremoval_index     ) { ch_reference_index = file(params.shortread_hostremoval_index    ) } else { ch_reference_index = [] }
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -49,6 +52,7 @@ include { INPUT_CHECK             } from '../subworkflows/local/input_check'
 include { DB_CHECK                } from '../subworkflows/local/db_check'
 include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
 include { LONGREAD_PREPROCESSING  } from '../subworkflows/local/longread_preprocessing'
+include { SHORTREAD_HOSTREMOVAL   } from '../subworkflows/local/shortread_hostremoval'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -120,17 +124,24 @@ workflow TAXPROFILER {
     if ( params.longread_clip ) {
         ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
                                         .map { it -> [ it[0], [it[1]] ] }
-    ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
-    } else {
+        ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
+    } else {SHORTREAD_HOSTREMOVAL
         ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
     }
 
+    if ( params.shortread_hostremoval ) {
+        ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_preprocessed, ch_reference, ch_reference_index ).reads
+        ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
+    } else {
+        ch_shortreads_hostremoved = ch_shortreads_preprocessed
+    }
+
     /*
         COMBINE READS WITH POSSIBLE DATABASES
     */
 
     // e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
-    ch_input_for_profiling = ch_shortreads_preprocessed
+    ch_input_for_profiling = ch_shortreads_hostremoved
             .mix( ch_longreads_preprocessed )
             .combine(DB_CHECK.out.dbs)
             .branch {
@@ -196,9 +207,15 @@ workflow TAXPROFILER {
     if (params.shortread_clipmerge) {
         ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.mqc)
     }
+
+    if (params.shortread_hostremoval) {
+        ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
+    }
+
     if (params.longread_clip) {
         ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
     }
+
     if (params.run_kraken2) {
         ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]))
         ch_versions = ch_versions.mix(KRAKEN2_KRAKEN2.out.versions.first())