Merge pull request #34 from nf-core/adapterremoval

Add AdapterRemoval as alternative trimer/merger

.github/workflows/ci.yml

@@ -28,6 +28,10 @@ jobs:
           # Test latest edge release of Nextflow
           - NXF_VER: ""
             NXF_EDGE: "1"
+        parameters:
+          - "--shortread_clipmerge_tool fastp"
+          - "--shortread_clipmerge_tool adapterremoval"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -47,6 +51,6 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
 
 #

CITATIONS.md

@@ -13,9 +13,26 @@
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
-* [Porechop](https://github.com/rrwick/Porechop)
+- [fastp](https://doi.org/10.1093/bioinformatics/bty560)
+
+  > Chen, Shifu, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018. “Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor.” Bioinformatics 34 (17): i884-90. 10.1093/bioinformatics/bty560.
+
+- [AdapterRemoval2](https://doi.org/10.1186/s13104-016-1900-2)
+
+  > Schubert, Mikkel, Stinus Lindgreen, and Ludovic Orlando. 2016. “AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging.” BMC Research Notes 9 (February): 88. doi:10.1186/s13104-016-1900-2.
+
+- [Porechop](https://github.com/rrwick/Porechop)
+
+- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)
+
+  > 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.
+
+- [MALT](https://doi.org/10.1038/s41559-017-0446-6)
+
+  > Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. “Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico.” Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.
 
 ## Software packaging/containerisation tools
 

conf/modules.config

@@ -62,18 +62,15 @@ process {
         ]
     }
 
-    withName: FASTP {
-        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+    withName: FASTP_SINGLE {
         ext.args   = [
-            // collapsing options - option to retain singletons
-            params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
             // trimming options
             params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
             params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
-            !{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
             // filtering options
             "--length_required ${params.shortread_clipmerge_minlength}"
         ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/fastp" },
             mode: 'copy',
@@ -81,6 +78,61 @@ process {
         ]
     }
 
+    withName: FASTP_PAIRED {
+        ext.args   = [
+            // collapsing options - option to retain singletons
+            params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
+            // trimming options
+            params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
+            params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
+            params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
+            // filtering options
+            "--length_required ${params.shortread_clipmerge_minlength}"
+        ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/fastp" },
+            mode: 'copy',
+            pattern: '*.fastq.gz'
+        ]
+    }
+
+    withName: ADAPTERREMOVAL_SINGLE {
+        ext.args   = [
+            // trimming options
+            params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
+            params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
+            // filtering options
+            "--minlength ${params.shortread_clipmerge_minlength}"
+        ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/adapterremoval" },
+            mode: 'copy',
+            pattern: '*.fastq.gz'
+        ]
+    }
+
+    withName: ADAPTERREMOVAL_PAIRED {
+        ext.args   = [
+            // collapsing options
+            params.shortread_clipmerge_mergepairs ? "--collapse" : "",
+            // trimming options
+            params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
+            params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
+            params.shortread_clipmerge_adapter2 ? "--adapter2 ${params.shortread_clipmerge_adapter2}" : "",
+            // filtering options
+            "--minlength ${params.shortread_clipmerge_minlength}"
+        ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/adapterremoval" },
+            mode: 'copy',
+            pattern: '*.fastq.gz'
+        ]
+    }
+
+
     withName: PORECHOP {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
@@ -99,23 +151,23 @@ process {
     }
 
     withName: MALT_RUN {
+        ext.args = { "${meta.db_params}" }
+        ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/malt/${meta.db_name}" },
             mode: 'copy',
             pattern: '*.{rma6,tab,text,sam,log}'
         ]
-        ext.args = { "${meta.db_params}" }
-        ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
     }
 
     withName: KRAKEN2_KRAKEN2 {
+        ext.args = { "${meta.db_params}" }
+        ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}" },
             mode: 'copy',
             pattern: '*.{fastq.gz,txt}'
         ]
-        ext.args = { "${meta.db_params}" }
-        ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
     }
 
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {

modules.json

@@ -3,6 +3,9 @@
     "homePage": "https://github.com/nf-core/taxprofiler",
     "repos": {
         "nf-core/modules": {
+            "adapterremoval": {
+                "git_sha": "f0800157544a82ae222931764483331a81812012"
+            },
             "cat/fastq": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },

modules/nf-core/modules/adapterremoval/main.nf

@@ -0,0 +1,70 @@
+process ADAPTERREMOVAL {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
+        'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path(adapterlist)
+
+    output:
+    tuple val(meta), path("${prefix}.truncated.gz")            , optional: true, emit: singles_truncated
+    tuple val(meta), path("${prefix}.discarded.gz")            , optional: true, emit: discarded
+    tuple val(meta), path("${prefix}.pair1.truncated.gz")      , optional: true, emit: pair1_truncated
+    tuple val(meta), path("${prefix}.pair2.truncated.gz")      , optional: true, emit: pair2_truncated
+    tuple val(meta), path("${prefix}.collapsed.gz")            , optional: true, emit: collapsed
+    tuple val(meta), path("${prefix}.collapsed.truncated.gz")  , optional: true, emit: collapsed_truncated
+    tuple val(meta), path("${prefix}.paired.gz")               , optional: true, emit: paired_interleaved
+    tuple val(meta), path('*.log')                             , emit: log
+    path "versions.yml"                                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def list = adapterlist ? "--adapter-list ${adapterlist}" : ""
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    if (meta.single_end) {
+        """
+        AdapterRemoval  \\
+            --file1 $reads \\
+            $args \\
+            $adapterlist \\
+            --basename ${prefix} \\
+            --threads ${task.cpus} \\
+            --settings ${prefix}.log \\
+            --seed 42 \\
+            --gzip
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+        END_VERSIONS
+        """
+    } else {
+        """
+        AdapterRemoval  \\
+            --file1 ${reads[0]} \\
+            --file2 ${reads[1]} \\
+            $args \\
+            $adapterlist \\
+            --basename ${prefix} \\
+            --threads $task.cpus \\
+            --settings ${prefix}.log \\
+            --seed 42 \\
+            --gzip
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+        END_VERSIONS
+        """
+    }
+
+}

modules/nf-core/modules/adapterremoval/meta.yml

@@ -0,0 +1,90 @@
+name: adapterremoval
+description: Trim sequencing adapters and collapse overlapping reads
+keywords:
+  - trimming
+  - adapters
+  - merging
+  - fastq
+tools:
+  - adapterremoval:
+      description: The AdapterRemoval v2 tool for merging and clipping reads.
+      homepage: https://github.com/MikkelSchubert/adapterremoval
+      documentation: https://adapterremoval.readthedocs.io
+      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.
+      pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+  - adapterlist:
+      type: file
+      description: Optional text file containing list of adapters to look for for removal
+        with one adapter per line. Otherwise will look for default adapters (see
+        AdapterRemoval man page), or can be modified to remove user-specified
+        adapters via ext.args.
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - singles_truncated:
+      type: file
+      description: |
+        Adapter trimmed FastQ files of either single-end reads, or singleton
+        'orphaned' reads from merging of paired-end data (i.e., one of the pair
+        was lost due to filtering thresholds).
+      pattern: "*.truncated.gz"
+  - discarded:
+      type: file
+      description: |
+        Adapter trimmed FastQ files of reads that did not pass filtering
+        thresholds.
+      pattern: "*.discarded.gz"
+  - pair1_truncated:
+      type: file
+      description: |
+        Adapter trimmed R1 FastQ files of paired-end reads that did not merge
+        with their respective R2 pair due to long templates. The respective pair
+        is stored in 'pair2_truncated'.
+      pattern: "*.pair1.truncated.gz"
+  - pair2_truncated:
+      type: file
+      description: |
+        Adapter trimmed R2 FastQ files of paired-end reads that did not merge
+        with their respective R1 pair due to long templates. The respective pair
+        is stored in 'pair1_truncated'.
+      pattern: "*.pair2.truncated.gz"
+  - collapsed:
+      type: file
+      description: |
+        Collapsed FastQ of paired-end reads that successfully merged with their
+        respective R1 pair but were not trimmed.
+      pattern: "*.collapsed.gz"
+  - collapsed_truncated:
+      type: file
+      description: |
+        Collapsed FastQ of paired-end reads that successfully merged with their
+        respective R1 pair and were trimmed of adapter due to sufficient overlap.
+      pattern: "*.collapsed.truncated.gz"
+  - log:
+      type: file
+      description: AdapterRemoval log file
+      pattern: "*.log"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@maxibor"
+  - "@jfy133"

nextflow.config

@@ -59,7 +59,7 @@ params {
     shortread_clipmerge_tool                = 'fastp'
     shortread_clipmerge_skipadaptertrim     = false
     shortread_clipmerge_mergepairs          = false
-    shortread_clipmerge_excludeunmerged     = true
+    shortread_clipmerge_excludeunmerged     = false
     shortread_clipmerge_adapter1            = null
     shortread_clipmerge_adapter2            = null
     shortread_clipmerge_minlength           = 15

nextflow_schema.json

@@ -267,7 +267,7 @@
         },
         "shortread_clipmerge_excludeunmerged": {
             "type": "boolean",
-            "default": true
+            "default": false
         },
         "longread_clip": {
             "type": "boolean"
@@ -284,7 +284,8 @@
         },
         "shortread_clipmerge_tool": {
             "type": "string",
-            "default": "fastp"
+            "default": "fastp",
+            "enum": ["fastp", "adapterremoval"]
         },
         "shortread_clipmerge_skipadaptertrim": {
             "type": "boolean"
@@ -294,11 +295,11 @@
         },
         "shortread_clipmerge_adapter1": {
             "type": "string",
-            "default": null
+            "default": "None"
         },
         "shortread_clipmerge_adapter2": {
             "type": "string",
-            "default": null
+            "default": "None"
         },
         "shortread_clipmerge_minlength": {
             "type": "integer",

subworkflows/local/db_check.nf

@@ -18,9 +18,7 @@ workflow DB_CHECK {
     parsed_samplesheet = DATABASE_CHECK ( dbsheet )
         .csv
         .splitCsv ( header:true, sep:',' )
-        .dump(tag: "db_split_csv_out")
         .map { create_db_channels(it) }
-        .dump(tag: "db_channel_prepped")
 
     ch_dbs_for_untar = parsed_samplesheet
         .branch {

subworkflows/local/input_check.nf

@@ -12,7 +12,6 @@ workflow INPUT_CHECK {
     parsed_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
         .csv
         .splitCsv ( header:true, sep:',' )
-        .dump(tag: "input_split_csv_out")
         .branch {
             fasta: it['fasta'] != ''
             nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
@@ -21,17 +20,14 @@ workflow INPUT_CHECK {
 
     parsed_samplesheet.fastq
         .map { create_fastq_channel(it) }
-        .dump(tag: "fastq_channel_init")
         .set { fastq }
 
     parsed_samplesheet.nanopore
         .map { create_fastq_channel(it) }
-        .dump(tag: "fastq_nanopore_channel_init")
         .set { nanopore }
 
     parsed_samplesheet.fasta
         .map { create_fasta_channel(it) }
-        .dump(tag: "fasta_channel_init")
         .set { fasta }
 
     emit:

subworkflows/local/longread_preprocessing.nf

@@ -16,7 +16,6 @@ workflow LONGREAD_PREPROCESSING {
     PORECHOP ( reads )
 
     ch_processed_reads = PORECHOP.out.reads
-                                .dump(tag: "pre_fastqc_check")
                                 .map {
                                         meta, reads ->
                                         def meta_new = meta.clone()

subworkflows/local/shortread_adapterremoval.nf

@@ -0,0 +1,86 @@
+/*
+Process short raw reads with AdapterRemoval
+*/
+
+include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE       } from '../../modules/nf-core/modules/adapterremoval/main'
+include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED       } from '../../modules/nf-core/modules/adapterremoval/main'
+include { CAT_FASTQ                                     } from '../../modules/nf-core/modules/cat/fastq/main'
+
+workflow SHORTREAD_ADAPTERREMOVAL {
+
+    take:
+    reads // [[meta], [reads]]
+
+    main:
+    ch_versions = Channel.empty()
+    ch_multiqc_files      = Channel.empty()
+
+    ch_input_for_adapterremoval = reads
+                                    .branch{
+                                        single: it[0].single_end
+                                        paired: !it[0].single_end
+                                    }
+
+    ADAPTERREMOVAL_SINGLE ( ch_input_for_adapterremoval.single, [] )
+    ADAPTERREMOVAL_PAIRED ( ch_input_for_adapterremoval.paired, [] )
+
+    // due to the slightly ugly output implementation of the current AdapterRemoval2 version, each file
+    // has to be exported in a separate channel, and we must manually recombine when necessary
+
+    if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
+        ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
+                                                .mix(
+                                                    ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
+                                                    ADAPTERREMOVAL_PAIRED.out.singles_truncated,
+                                                    ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
+                                                    ADAPTERREMOVAL_PAIRED.out.pair2_truncated
+                                                    )
+                                                .map {
+                                                    meta, reads ->
+                                                        def meta_new = meta.clone()
+                                                        meta_new.single_end = true
+
+                                                        [ meta_new, reads ]
+                                                    }
+                                                    .groupTuple()
+
+        ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
+                                            .mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
+
+    } else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
+        ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
+                                                .mix( ADAPTERREMOVAL_PAIRED.out.collapsed_truncated )
+                                                .map {
+                                                    meta, reads ->
+                                                        def meta_new = meta.clone()
+                                                        meta_new['single_end'] = true
+
+                                                        [ meta_new, reads ]
+                                                    }
+                                                    .groupTuple(by: 0)
+
+        ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
+                                            .mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
+
+    } else {
+
+        ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.pair1_truncated
+                                                .join( ADAPTERREMOVAL_PAIRED.out.pair2_truncated )
+                                                .groupTuple()
+                                                .map { meta, pair1, pair2 ->
+                                                        [ meta, [ pair1, pair2 ].flatten() ]
+                                                }
+                                            .mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
+    }
+
+    ch_processed_reads = ch_adapterremoval_reads_prepped
+
+    ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
+    ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
+    ch_multiqc_files = ch_multiqc_files.mix( ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]}, ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]} )
+
+    emit:
+    reads    = ch_processed_reads   // channel: [ val(meta), [ reads ] ]
+    versions = ch_versions          // channel: [ versions.yml ]
+    mqc      = ch_multiqc_files
+}

subworkflows/local/shortread_fastp.nf

@@ -14,15 +14,11 @@ workflow SHORTREAD_FASTP {
     ch_multiqc_files      = Channel.empty()
 
     ch_input_for_fastp = reads
-                            .dump(tag: "pre-fastp_branch")
                             .branch{
                                 single: it[0]['single_end'] == true
                                 paired: it[0]['single_end'] == false
                             }
 
-    ch_input_for_fastp.single.dump(tag: "input_fastp_single")
-    ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
-
     FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
     // Last parameter here turns on merging of PE data
     FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_clipmerge_mergepairs )
@@ -46,13 +42,11 @@ workflow SHORTREAD_FASTP {
     ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
     ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
 
-    ch_processed_reads = ch_fastp_reads_prepped.dump(tag: "ch_fastp_reads_prepped")
+    ch_processed_reads = ch_fastp_reads_prepped
 
     ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json.collect{it[1]} )
     ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} )
 
-    ch_multiqc_files.dump(tag: "preprocessing_fastp_mqc_final")
-
     emit:
     reads    = ch_processed_reads   // channel: [ val(meta), [ reads ] ]
     versions = ch_versions          // channel: [ versions.yml ]

subworkflows/local/shortread_preprocessing.nf

@@ -4,6 +4,7 @@
 
 
 include { SHORTREAD_FASTP             } from './shortread_fastp'
+include { SHORTREAD_ADAPTERREMOVAL    } from './shortread_adapterremoval'
 include { FASTQC as FASTQC_PROCESSED       } from '../../modules/nf-core/modules/fastqc/main'
 
 workflow SHORTREAD_PREPROCESSING {
@@ -18,6 +19,10 @@ workflow SHORTREAD_PREPROCESSING {
         ch_processed_reads = SHORTREAD_FASTP ( reads ).reads
         ch_versions        =  ch_versions.mix( SHORTREAD_FASTP.out.versions )
         ch_multiqc_files   =  ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
+    } else if ( params.shortread_clipmerge_tool == "adapterremoval" ) {
+        ch_processed_reads = SHORTREAD_ADAPTERREMOVAL ( reads ).reads
+        ch_versions        = ch_versions.mix( SHORTREAD_ADAPTERREMOVAL.out.versions )
+        ch_multiqc_files   = ch_multiqc_files.mix( SHORTREAD_ADAPTERREMOVAL.out.mqc )
     } else {
         ch_processed_reads = reads
     }

workflows/taxprofiler.nf

@@ -18,6 +18,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 if (params.input    ) { ch_input     = file(params.input)     } else { exit 1, 'Input samplesheet not specified!' }
 if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
 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"
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -126,7 +127,6 @@ workflow TAXPROFILER {
     ch_input_for_profiling = ch_shortreads_preprocessed
             .mix( ch_longreads_preprocessed )
             .combine(DB_CHECK.out.dbs)
-            .dump(tag: "reads_plus_db_clean")
             .branch {
                 malt:    it[2]['tool'] == 'malt'
                 kraken2: it[2]['tool'] == 'kraken2'
@@ -141,9 +141,7 @@ workflow TAXPROFILER {
     // loading takes a long time, so we only want to run it once per database
     // TODO document somewhere we only accept illumina short reads for MALT?
     ch_input_for_malt =  ch_input_for_profiling.malt
-                            .dump(tag: "input_to_malt_prefilter")
                             .filter { it[0]['instrument_platform'] == 'ILLUMINA' }
-                            .dump(tag: "input_to_malt_postfilter")
                             .map {
                                 it ->
                                     def temp_meta =  [ id: it[2]['db_name']]  + it[2]
@@ -151,7 +149,6 @@ workflow TAXPROFILER {
                                     [ temp_meta, it[1], db ]
                             }
                             .groupTuple(by: [0,2])
-                            .dump(tag: "input_to_malt")
                             .multiMap {
                                 it ->
                                     reads: [ it[0], it[1].flatten() ]
@@ -160,7 +157,6 @@ workflow TAXPROFILER {
 
     // We can run Kraken2 one-by-one sample-wise
     ch_input_for_kraken2 =  ch_input_for_profiling.kraken2
-                            .dump(tag: "input_to_kraken")
                             .multiMap {
                                 it ->
                                     reads: [ it[0] + it[2], it[1] ]