Merge branch 'dev' into database-untar

CITATIONS.md

@@ -15,6 +15,8 @@
 * [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)
+
 ## 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
 
 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 2. Performs optional read pre-processing
-   - Adapter clipping and merging
+   - Adapter clipping and merging (short, and nanopore reads)
    - Low complexity filtering
    - Host read removal
    - Run merging

bin/check_samplesheet.py

@@ -173,7 +173,7 @@ def check_samplesheet(file_in, file_out):
             ## Auto-detect paired-end/single-end
             if sample and fastq_1 and fastq_2:  ## Paired-end short reads
                 sample_info.extend(["0", fastq_1, fastq_2, fasta])
-            elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
+            elif sample and fastq_1 and not fastq_2:  ## Single-end short/long fastq reads
                 sample_info.extend(["1", fastq_1, fastq_2, fasta])
             elif (
                 sample and fasta and not fastq_1 and not fastq_2

conf/modules.config

@@ -41,7 +41,7 @@ process {
         // TODO also include option to NOT merge
         ext.args   = [
             { ${meta.single_end} } == 0 ? "-m" : '',
-            params.fastp_exclude_unmerged ? '' : "--include_unmerged"
+            params.shortread_excludeunmerged ? '' : "--include_unmerged"
         ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/fastp" },
@@ -50,6 +50,15 @@ process {
         ]
     }
 
+    withName: PORECHOP {
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/porechop" },
+            mode: 'copy',
+            pattern: '*.fastq.gz'
+        ]
+    }
+
     withName: FASTQC_POST {
         ext.args = '--quiet'
         ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
@@ -75,7 +84,7 @@ process {
             pattern: '*.{rma6,tab,text,sam,log}'
         ]
         ext.args = { "${meta.db_params}" }
-        ext.when = params.run_malt
+        ext.prefix = { "${meta.id}-${meta.db_name}" }
     }
 
     withName: KRAKEN2_KRAKEN2 {
@@ -85,7 +94,6 @@ process {
             pattern: '*.{fastq.gz,txt}'
         ]
         ext.args = { "${meta.db_params}" }
-        ext.when = params.run_kraken2
         ext.prefix = { "${meta.id}-${meta.db_name}" }
     }
 

docs/usage.md

@@ -44,11 +44,11 @@ TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,
 TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,
 ```
 
-| Column         | Description                                                                                                                                                                            |
+| Column    | Description                                                                                                                                                                            |
-|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `sample`       | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
+| `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
-| `fastq_1`      | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
+| `fastq_1` | Full path to FastQ file for Illumina short reads 1 or Nanopore reads. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                           |
-| `fastq_2`      | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
+| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 

modules.json

@@ -26,6 +26,8 @@
             },
             "untar": {
                 "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
+            "porechop": {
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             }
         }
     }

modules/nf-core/modules/porechop/main.nf

@@ -0,0 +1,35 @@
+process PORECHOP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
+        'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    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}"
+    """
+    porechop \\
+        -i $reads \\
+        -t $task.cpus \\
+        $args \\
+        -o ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        porechop: \$( porechop --version )
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,50 @@
+name: porechop
+description: Adapter removal and demultiplexing of Oxford Nanopore reads
+keywords:
+  - adapter
+  - nanopore
+  - demultiplexing
+tools:
+  - porechop:
+      description: Adapter removal and demultiplexing of Oxford Nanopore reads
+      homepage: "https://github.com/rrwick/Porechop"
+      documentation: "https://github.com/rrwick/Porechop"
+      tool_dev_url: "https://github.com/rrwick/Porechop"
+      doi: "10.1099/mgen.0.000132"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: fastq/fastq.gz file
+      pattern: "*.{fastq,fastq.gz,fq,fq.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: Demultiplexed and/or adapter-trimmed fastq.gz file
+      pattern: "*.{fastq.gz}"
+
+authors:
+  - "@ggabernet"
+  - "@jasmezz"
+  - "@d4straub"
+  - "@LaurenceKuhl"
+  - "@SusiJo"
+  - "@jonasscheid"
+  - "@jonoave"
+  - "@GokceOGUZ"

nextflow.config

@@ -55,8 +55,9 @@ params {
     databases = null
 
     // FASTQ preprocessing
-    fastp_clip_merge           = false
+    shortread_clipmerge           = false
-    fastp_exclude_unmerged     = true
+    shortread_excludeunmerged        = true
+    longread_clip                 = false
 
     // MALT
     run_malt                   = false

subworkflows/local/input_check.nf

@@ -15,14 +15,20 @@ workflow INPUT_CHECK {
         .dump(tag: "input_split_csv_out")
         .branch {
             fasta: it['fasta'] != ''
+            nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
             fastq: true
         }
 
     parsed_samplesheet.fastq
-        .map { create_fastq_channels(it) }
+        .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_channels(it) }
         .dump(tag: "fasta_channel_init")
@@ -30,6 +36,7 @@ workflow INPUT_CHECK {
 
     emit:
     fastq                                     // channel: [ val(meta), [ reads ] ]
+    nanopore                                  // channel: [ val(meta), [ reads ] ]
     fasta                                     // channel: [ val(meta), fasta ]
     versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
 }
@@ -51,10 +58,17 @@ def create_fastq_channels(LinkedHashMap row) {
     if (meta.single_end) {
         fastq_meta = [ meta, [ file(row.fastq_1) ] ]
     } else {
-        if (!file(row.fastq_2).exists()) {
+        if (meta.instrument_platform == 'OXFORD_NANOPORE') {
-            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
+            if (row.fastq_2 != '') {
+                exit 1, "ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}"
+            }
+            fastq_meta = [ meta, [ file(row.fastq_1) ] ]
+        } else {
+            if (!file(row.fastq_2).exists()) {
+                exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
+            }
+            fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
         }
-        fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
     }
     return fastq_meta
 }

subworkflows/local/longread_preprocessing.nf

@@ -0,0 +1,34 @@
+
+include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
+include { PORECHOP              } from '../../modules/nf-core/modules/porechop/main'
+
+workflow LONGREAD_PREPROCESSING {
+    take:
+    reads
+
+    main:
+    ch_versions      = Channel.empty()
+    ch_multiqc_files = Channel.empty()
+
+    PORECHOP ( reads )
+
+    ch_processed_reads = PORECHOP.out.reads
+                                .dump(tag: "pre_fastqc_check")
+                                .map {
+                                        meta, reads ->
+                                        def meta_new = meta.clone()
+                                        meta_new['single_end'] = 1
+                                        [ meta_new, reads ]
+                                    }
+
+    FASTQC_POST ( PORECHOP.out.reads )
+    ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
+    ch_multiqc_files = ch_multiqc_files.mix( FASTQC_POST.out.zip.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_preprocessing.nf

@@ -7,7 +7,7 @@ include { FASTP as FASTP_SINGLE       } from '../../modules/nf-core/modules/fast
 include { FASTP as FASTP_PAIRED       } from '../../modules/nf-core/modules/fastp/main'
 include { FASTQC as FASTQC_POST       } from '../../modules/nf-core/modules/fastqc/main'
 
-workflow FASTQ_PREPROCESSING {
+workflow SHORTREAD_PREPROCESSING {
     take:
     reads // file: /path/to/samplesheet.csv
 
@@ -23,7 +23,7 @@ workflow FASTQ_PREPROCESSING {
     // TODO move to subworkflow
 
 
-    if ( params.fastp_clip_merge ) {
+    if ( params.shortread_clipmerge ) {
 
         ch_input_for_fastp = reads
                                 .dump(tag: "pre-fastp_branch")

workflows/taxprofiler.nf

@@ -39,8 +39,8 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
 include { INPUT_CHECK         } from '../subworkflows/local/input_check'
 
 include { DB_CHECK            } from '../subworkflows/local/db_check'
-include { FASTQ_PREPROCESSING } from '../subworkflows/local/preprocessing'
+include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
-
+include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -89,7 +89,7 @@ workflow TAXPROFILER {
     // MODULE: Run FastQC
     //
     FASTQC (
-        INPUT_CHECK.out.fastq
+        INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
     )
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
@@ -100,14 +100,22 @@ workflow TAXPROFILER {
     //
     // PERFORM PREPROCESSING
     //
-    if ( params.fastp_clip_merge ) {
+    if ( params.shortread_clipmerge ) {
-        FASTQ_PREPROCESSING ( INPUT_CHECK.out.fastq )
+        SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq )
+    }
+
+    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_longreads_preprocessed = INPUT_CHECK.out.nanopore
     }
 
     //
     // PERFORM RUN MERGING
     //
-    ch_processed_for_combine = FASTQ_PREPROCESSING.out.reads
+    ch_processed_for_combine = SHORTREAD_PREPROCESSING.out.reads
         .dump(tag: "prep_for_combine_grouping")
         .map {
             meta, reads ->
@@ -134,6 +142,7 @@ workflow TAXPROFILER {
 
     // 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_reads_for_profiling
+            .mix( ch_longreads_preprocessed )
             .combine(DB_CHECK.out.dbs)
             .dump(tag: "reads_plus_db")
             .branch {
@@ -175,9 +184,13 @@ workflow TAXPROFILER {
     //
     // RUN PROFILING
     //
-    MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
+    if ( params.run_malt ) {
-    KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db  )
+        MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
+    }
 
+    if ( params.run_kraken2 ) {
+        KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db  )
+    }
 
     //
     // MODULE: MultiQC
@@ -191,8 +204,12 @@ 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(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
-    if (params.fastp_clip_merge) {
+
-        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_PREPROCESSING.out.mqc)
+    if (params.shortread_clipmerge) {
+        ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.mqc)
+    }
+    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([]))