Merge branch 'dev' into support-aligned-reads

.github/workflows/ci.yml

@@ -29,18 +29,18 @@ jobs:
           - NXF_VER: ""
             NXF_EDGE: "1"
         parameters:
-          - "--perform_longread_clip false"
-          - "--perform_shortread_clipmerge false"
-          - "--shortread_clipmerge_tool fastp"
-          - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
-          - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
-          - "--shortread_clipmerge_tool adapterremoval"
-          - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
-          - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
+          - "--perform_longread_qc false"
+          - "--perform_shortread_qc false"
+          - "--shortread_qc_tool fastp"
+          - "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
+          - "--shortread_qc_tool fastp --shortread_qc_mergepairs"
+          - "--shortread_qc_tool adapterremoval"
+          - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
+          - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
           - "--shortread_complexityfilter_tool bbduk"
           - "--shortread_complexityfilter_tool prinseqplusplus"
           - "--perform_runmerging"
-          - "--perform_runmerging --shortread_clipmerge_mergepairs"
+          - "--perform_runmerging --shortread_qc_mergepairs"
           - "--shortread_complexityfilter false --perform_shortread_hostremoval"
 
     steps:

CITATIONS.md

@@ -56,6 +56,8 @@
 
 > Buchfink, Benjamin, Chao Xie, and Daniel H. Huson. 2015. “Fast and Sensitive Protein Alignment Using DIAMOND.” Nature Methods 12 (1): 59-60. doi: 10.1038/nmeth.3176.
 
+- [FILTLONG](https://github.com/rrwick/Filtlong)
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

conf/modules.config

@@ -51,10 +51,10 @@ process {
     withName: FASTP_SINGLE {
         ext.args   = [
             // trimming options
-            params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
-            params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
+            params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
+            params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
             // filtering options
-            "--length_required ${params.shortread_clipmerge_minlength}",
+            "--length_required ${params.shortread_qc_minlength}",
             (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
         ].join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
@@ -69,13 +69,13 @@ process {
     withName: FASTP_PAIRED {
         ext.args   = [
             // collapsing options - option to retain singletons
-            params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
+            params.shortread_qc_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",
+            params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
+            params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
+            params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
             // filtering options
-            "--length_required ${params.shortread_clipmerge_minlength}",
+            "--length_required ${params.shortread_qc_minlength}",
             params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
         ].join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
@@ -90,10 +90,10 @@ process {
     withName: ADAPTERREMOVAL_SINGLE {
         ext.args   = [
             // trimming options
-            params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
-            params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
+            params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
+            params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
             // filtering options
-            "--minlength ${params.shortread_clipmerge_minlength}"
+            "--minlength ${params.shortread_qc_minlength}"
         ].join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
@@ -107,13 +107,13 @@ process {
     withName: ADAPTERREMOVAL_PAIRED {
         ext.args   = [
             // collapsing options
-            params.shortread_clipmerge_mergepairs ? "--collapse" : "",
+            params.shortread_qc_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}" : "",
+            params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
+            params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
+            params.shortread_qc_adapter2 ? "--adapter2 ${params.shortread_qc_adapter2}" : "",
             // filtering options
-            "--minlength ${params.shortread_clipmerge_minlength}"
+            "--minlength ${params.shortread_qc_minlength}"
         ].join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
@@ -134,6 +134,22 @@ process {
         ]
     }
 
+    withName: FILTLONG {
+        ext.args = [
+            "--min_length ${params.longread_qc_minlength}",
+            "--keep_percent ${params.longread_qc_keep_percent}",
+            "--target_bases ${params.longread_qc_target_bases}"
+        ]
+        .join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
+        publishDir = [
+            path: { "${params.outdir}/filtlong" },
+            mode: params.publish_dir_mode,
+            pattern: '*.fastq.gz',
+            enabled: params.save_preprocessed_reads
+        ]
+    }
+
     withName: BOWTIE2_BUILD {
         publishDir = [
             path: { "${params.outdir}/bowtie2/build" },

conf/test.config

@@ -24,8 +24,8 @@ params {
     // 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'
-    perform_shortread_clipmerge           = true
-    perform_longread_clip                 = false
+    perform_shortread_qc                  = true
+    perform_longread_qc                   = true
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true

conf/test_nopreprocessing.config

@@ -24,8 +24,8 @@ params {
     // 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'
-    perform_shortread_clipmerge           = false
-    perform_longread_clip                 = false
+    perform_shortread_qc                  = false
+    perform_longread_qc                   = false
     perform_shortread_complexityfilter    = false
     perform_shortread_hostremoval         = false
     perform_longread_hostremoval          = false

conf/test_noprofiling.config

@@ -24,8 +24,8 @@ params {
     // 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'
-    perform_shortread_clipmerge           = true
-    perform_longread_clip                 = true
+    perform_shortread_qc                  = true
+    perform_longread_qc                   = true
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true

docs/usage.md

@@ -162,16 +162,16 @@ nf-core/taxprofiler offers four main preprocessing steps
 
 #### Read Processing
 
-Raw sequencing read processing in the form of adapter clipping and paired-end read merging can be activated via the `--perform_shortread_clipmerge` or `--perform_longread_clip` flags.
+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.
 
 There are currently two options for short-read preprocessing: `fastp` or `adapterremoval`.
 
-For adapter clipping, you can either rely on tool default adapter sequences, or supply your own adapters (`--shortread_clipmerge_adapter1` and `--shortread_clipmerge_adapter2`)
-By default, paired-end merging is not activated and paired-end profiling is performed where supported otherwise pairs will be independently profiled. If paired-end merging is activated you can also specify whether to exclude unmerged reads in the reads sent for profiling (`--shortread_clipmerge_mergepairs` and `--shortread_clipmerge_excludeunmerged`).
-You can also turn off clipping and only perform paired-end merging, if requested. This can be useful when processing data downloaded from the ENA, SRA, or DDBJ (`--shortread_clipmerge_skipadaptertrim`).
-Both tools support length filtering of reads and can be tuned with `--shortread_clipmerge_minlength`. Performing length filtering can be useful to remove short (often low sequencing complexity) sequences that result in unspecific classification and therefore slow down runtime during profiling, with minimal gain.
+For adapter clipping, you can either rely on tool default adapter sequences, or supply your own adapters (`--shortread_qc_adapter1` and `--shortread_qc_adapter2`)
+By default, paired-end merging is not activated and paired-end profiling is performed where supported otherwise pairs will be independently profiled. If paired-end merging is activated you can also specify whether to exclude unmerged reads in the reads sent for profiling (`--shortread_qc_mergepairs` and `--shortread_qc_excludeunmerged`).
+You can also turn off clipping and only perform paired-end merging, if requested. This can be useful when processing data downloaded from the ENA, SRA, or DDBJ (`--shortread_qc_skipadaptertrim`).
+Both tools support length filtering of reads and can be tuned with `--shortread_qc_minlength`. Performing length filtering can be useful to remove short (often low sequencing complexity) sequences that result in unspecific classification and therefore slow down runtime during profiling, with minimal gain.
 
 There is currently one option for long-read Oxford Nanopore processing: `porechop`.
 

modules.json

@@ -36,6 +36,9 @@
             "fastqc": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "filtlong": {
+                "git_sha": "089f761f0bf79c4a486f1df9b6205f650196a2c1"
+            },
             "kaiju/kaiju": {
                 "git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
             },

modules/nf-core/modules/filtlong/main.nf

@@ -0,0 +1,37 @@
+process FILTLONG {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' :
+        'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }"
+
+    input:
+    tuple val(meta), path(shortreads), path(longreads)
+
+    output:
+    tuple val(meta), path("*.fastq.gz"), emit: reads
+    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 short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
+    if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
+    """
+    filtlong \\
+        $short_reads \\
+        $args \\
+        $longreads \\
+        | gzip -n > ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        filtlong: \$( filtlong --version | sed -e "s/Filtlong v//g" )
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,50 @@
+name: filtlong
+description: Filtlong filters long reads based on quality measures or short read data.
+keywords:
+  - nanopore
+  - quality control
+  - QC
+  - filtering
+  - long reads
+  - short reads
+tools:
+  - filtlong:
+      description: Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
+      homepage: https://anaconda.org/bioconda/filtlong
+      documentation: None
+      tool_dev_url: https://github.com/rrwick/Filtlong
+      doi: ""
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - shortreads:
+      type: file
+      description: fastq file
+      pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+  - longreads:
+      type: file
+      description: fastq file
+      pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+
+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"
+  - reads:
+      type: file
+      description: Filtered (compressed) fastq file
+      pattern: "*.fastq.gz"
+
+authors:
+  - "@d4straub"

nextflow.config

@@ -55,16 +55,23 @@ params {
     databases = null
 
     // FASTQ preprocessing
-    perform_shortread_clipmerge             = false
-    shortread_clipmerge_tool                = 'fastp'
-    shortread_clipmerge_skipadaptertrim     = false
-    shortread_clipmerge_mergepairs          = false
-    shortread_clipmerge_excludeunmerged     = false
-    shortread_clipmerge_adapter1            = null
-    shortread_clipmerge_adapter2            = null
-    shortread_clipmerge_minlength           = 15
-    perform_longread_clip                   = false
-    save_preprocessed_reads                 = false
+    perform_shortread_qc             = false
+    shortread_qc_tool                = 'fastp'
+    shortread_qc_skipadaptertrim     = false
+    shortread_qc_mergepairs          = false
+    shortread_qc_excludeunmerged     = false
+    shortread_qc_adapter1            = null
+    shortread_qc_adapter2            = null
+    shortread_qc_minlength           = 15
+
+    perform_longread_qc              = false
+    longread_qc_run_clip             = false
+    longread_qc_run_filter           = false
+    longread_qc_minlength            = 1000
+    longread_qc_keep_percent        = 90
+    longread_qc_target_bases         = 500000000
+
+    save_preprocessed_reads          = false
 
     // Complexity filtering
     perform_shortread_complexityfilter                   = false
@@ -193,6 +200,7 @@ profiles {
 }
 
 // Load igenomes.config if required
+
 if (!params.igenomes_ignore) {
     includeConfig 'conf/igenomes.config'
 } else {

nextflow_schema.json

@@ -262,7 +262,7 @@
             "type": "string",
             "default": "None"
         },
-        "shortread_clipmerge_excludeunmerged": {
+        "shortread_qc_excludeunmerged": {
             "type": "boolean"
         },
         "run_malt": {
@@ -282,26 +282,26 @@
             "type": "boolean",
             "description": "Enable MetaPhlAn for taxonomic profiling"
         },
-        "shortread_clipmerge_tool": {
+        "shortread_qc_tool": {
             "type": "string",
             "default": "fastp",
             "enum": ["fastp", "adapterremoval"]
         },
-        "shortread_clipmerge_skipadaptertrim": {
+        "shortread_qc_skipadaptertrim": {
             "type": "boolean"
         },
-        "shortread_clipmerge_mergepairs": {
+        "shortread_qc_mergepairs": {
             "type": "boolean"
         },
-        "shortread_clipmerge_adapter1": {
+        "shortread_qc_adapter1": {
             "type": "string",
             "default": "None"
         },
-        "shortread_clipmerge_adapter2": {
+        "shortread_qc_adapter2": {
             "type": "string",
             "default": "None"
         },
-        "shortread_clipmerge_minlength": {
+        "shortread_qc_minlength": {
             "type": "integer",
             "default": 15
         },
@@ -339,10 +339,10 @@
         "save_runmerged_reads": {
             "type": "boolean"
         },
-        "perform_shortread_clipmerge": {
+        "perform_shortread_qc": {
             "type": "boolean"
         },
-        "perform_longread_clip": {
+        "perform_longread_qc": {
             "type": "boolean"
         },
         "perform_shortread_complexityfilter": {
@@ -401,6 +401,24 @@
             "type": "integer",
             "default": 30
         },
+        "longread_qc_run_clip": {
+            "type": "boolean"
+        },
+        "longread_qc_run_filter": {
+            "type": "boolean"
+        },
+        "longread_qc_minlength": {
+            "type": "integer",
+            "default": 1000
+        },
+        "longread_qc_keep_percent": {
+            "type": "integer",
+            "default": 90
+        },
+        "longread_qc_target_bases": {
+            "type": "integer",
+            "default": 500000000
+        }
         "malt_save_reads": {
             "type": "boolean"
         },

subworkflows/local/longread_preprocessing.nf

@@ -4,6 +4,7 @@
 
 include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
 include { PORECHOP                   } from '../../modules/nf-core/modules/porechop/main'
+include { FILTLONG                   } from '../../modules/nf-core/modules/filtlong/main'
 
 workflow LONGREAD_PREPROCESSING {
     take:
@@ -13,21 +14,43 @@ workflow LONGREAD_PREPROCESSING {
     ch_versions      = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
-    PORECHOP ( reads )
+    if ( params.longread_qc_run_clip && !params.longread_qc_run_filter ) {
+        PORECHOP ( reads )
 
-    ch_processed_reads = PORECHOP.out.reads
-                                .map {
-                                        meta, reads ->
-                                        def meta_new = meta.clone()
-                                        meta_new['single_end'] = 1
-                                        [ meta_new, reads ]
-                                    }
+        ch_processed_reads = PORECHOP.out.reads
+                                        .map {
+                                                meta, reads ->
+                                                def meta_new = meta.clone()
+                                                meta_new['single_end'] = 1
+                                                [ meta_new, reads ]
 
-    FASTQC_PROCESSED ( PORECHOP.out.reads )
-    ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
+        ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
+                                            }
+    } else if ( !params.longread_qc_run_clip && params.longread_qc_run_filter ) {
+
+        ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
+        ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
+
+    } else {
+        PORECHOP ( reads )
+        ch_clipped_reads = PORECHOP.out.reads
+                                        .map {
+                                                meta, reads ->
+                                                def meta_new = meta.clone()
+                                                meta_new['single_end'] = 1
+                                                [ meta_new, reads ]
+                                        }
+
+        ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads
+
+        ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
+        ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
+
+    }
+
+    FASTQC_PROCESSED ( ch_processed_reads.dump(tag: "filtlong") )
     ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
 
-
     emit:
     reads    = ch_processed_reads   // channel: [ val(meta), [ reads ] ]
     versions = ch_versions          // channel: [ versions.yml ]

subworkflows/local/shortread_adapterremoval.nf

@@ -29,7 +29,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
      * has to be exported in a separate channel and we must manually recombine when necessary.
      */
 
-    if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
+    if ( params.shortread_qc_mergepairs && !params.shortread_qc_excludeunmerged ) {
 
         ch_concat_fastq = Channel.empty()
             .mix(
@@ -54,7 +54,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
         ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
             .mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
 
-    } else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
+    } else if ( params.shortread_qc_mergepairs && params.shortread_qc_excludeunmerged ) {
 
         ch_concat_fastq = Channel.empty()
             .mix(

subworkflows/local/shortread_fastp.nf

@@ -21,9 +21,9 @@ workflow SHORTREAD_FASTP {
 
     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 )
+    FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_qc_mergepairs )
 
-    if ( params.shortread_clipmerge_mergepairs ) {
+    if ( params.shortread_qc_mergepairs ) {
         ch_fastp_reads_prepped_pe = FASTP_PAIRED.out.reads_merged
                                         .map {
                                             meta, reads ->

subworkflows/local/shortread_preprocessing.nf

@@ -15,11 +15,11 @@ workflow SHORTREAD_PREPROCESSING {
     ch_versions       = Channel.empty()
     ch_multiqc_files  = Channel.empty()
 
-    if ( params.shortread_clipmerge_tool == "fastp" ) {
+    if ( params.shortread_qc_tool == "fastp" ) {
         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" ) {
+    } else if ( params.shortread_qc_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 )

workflows/taxprofiler.nf

@@ -20,10 +20,11 @@ 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] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
-if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
+if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
+if (params.shortread_qc_excludeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_qc_mergepairs"
+if ( (params.longread_qc_run_clip || params.longread_qc_run_filter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_run_clip or --longread_qc_run_filter requested but quality-control not turned on. Please specify --perform_long_qc"
 
-if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_clipmerge == false || params.shortread_clipmerge_tool != 'fastp' ))  exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_clipmerge and/or --shortread_clipmerge_tool 'fastp'"
+if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' ))  exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"
 
 if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input." }
 if (!params.hostremoval_reference && params.hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
@@ -118,14 +119,14 @@ workflow TAXPROFILER {
     /*
         SUBWORKFLOW: PERFORM PREPROCESSING
     */
-    if ( params.perform_shortread_clipmerge ) {
+    if ( params.perform_shortread_qc ) {
         ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
         ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
     } else {
         ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
     }
 
-    if ( params.perform_longread_clip ) {
+    if ( params.perform_longread_qc ) {
         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 )
@@ -229,11 +230,11 @@ workflow TAXPROFILER {
 
     ch_multiqc_files = ch_multiqc_files.mix(ch_taxprofiler_logo.ifEmpty([]))
 
-    if (params.perform_shortread_clipmerge) {
+    if (params.perform_shortread_qc) {
         ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
     }
 
-    if (params.perform_longread_clip) {
+    if (params.perform_longread_qc) {
         ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
     }