diff --git a/CITATIONS.md b/CITATIONS.md index 8f286b0..0eb8141 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -26,6 +26,8 @@ - [Porechop](https://github.com/rrwick/Porechop) +- [BBTools](http://sourceforge.net/projects/bbmap/) + - [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. diff --git a/conf/modules.config b/conf/modules.config index dc8b138..601f915 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -132,7 +132,6 @@ process { ] } - withName: PORECHOP { ext.prefix = { "${meta.id}_${meta.run_accession}" } publishDir = [ @@ -142,11 +141,17 @@ process { ] } - withName: CAT_FASTQ { + withName: BBMAP_BBDUK { + ext.args = [ + "entropy=${params.shortread_complexityfilter_bbduk_entropy}", + "entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}", + params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f" + ].join(' ').trim() + ext.prefix = { "${meta.id}-${meta.run_accession}" } publishDir = [ - path: { "${params.outdir}/prepared_sequences" }, - mode: 'copy', - pattern: '*.fastq.gz' + path: { "${params.outdir}/bbduk/" }, + mode: params.publish_dir_mode, + pattern: '*.{fastq.gz,log}' ] } diff --git a/modules.json b/modules.json index dcfbd3f..64e6c3c 100644 --- a/modules.json +++ b/modules.json @@ -6,6 +6,9 @@ "adapterremoval": { "git_sha": "f0800157544a82ae222931764483331a81812012" }, + "bbmap/bbduk": { + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" + }, "cat/fastq": { "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, diff --git a/modules/nf-core/modules/bbmap/bbduk/main.nf b/modules/nf-core/modules/bbmap/bbduk/main.nf new file mode 100644 index 0000000..0ae005e --- /dev/null +++ b/modules/nf-core/modules/bbmap/bbduk/main.nf @@ -0,0 +1,43 @@ +process BBMAP_BBDUK { + tag "$meta.id" + label 'process_medium' + + conda (params.enable_conda ? "bioconda::bbmap=38.90" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bbmap:38.90--he522d1c_1' : + 'quay.io/biocontainers/bbmap:38.90--he522d1c_1' }" + + input: + tuple val(meta), path(reads) + path contaminants + + output: + tuple val(meta), path('*.fastq.gz'), emit: reads + 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 prefix = task.ext.prefix ?: "${meta.id}" + def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}" + def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz" + def contaminants_fa = contaminants ? "ref=$contaminants" : '' + """ + maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g') + bbduk.sh \\ + -Xmx\$maxmem \\ + $raw \\ + $trimmed \\ + threads=$task.cpus \\ + $args \\ + $contaminants_fa \\ + &> ${prefix}.bbduk.log + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bbmap: \$(bbversion.sh) + END_VERSIONS + """ +} diff --git a/modules/nf-core/modules/bbmap/bbduk/meta.yml b/modules/nf-core/modules/bbmap/bbduk/meta.yml new file mode 100644 index 0000000..6abd3d9 --- /dev/null +++ b/modules/nf-core/modules/bbmap/bbduk/meta.yml @@ -0,0 +1,52 @@ +name: bbmap_bbduk +description: Adapter and quality trimming of sequencing reads +keywords: + - trimming + - adapter trimming + - quality trimming +tools: + - bbmap: + description: BBMap is a short read aligner, as well as various other bioinformatic tools. + homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ + documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ + tool_dev_url: None + doi: "" + licence: ["UC-LBL license (see package)"] + +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. + - contaminants: + type: file + description: | + Reference files containing adapter and/or contaminant sequences for sequence kmer matching + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: The trimmed/modified fastq reads + pattern: "*fastq.gz" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - log: + type: file + description: Bbduk log file + pattern: "*bbduk.log" + +authors: + - "@MGordon09" diff --git a/nextflow.config b/nextflow.config index 7be36a6..d57743a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -65,6 +65,13 @@ params { shortread_clipmerge_minlength = 15 longread_clip = false + // Complexity filtering + shortread_complexityfilter = false + shortread_complexityfilter_tool = 'bbduk' + shortread_complexityfilter_bbduk_entropy = 0.3 + shortread_complexityfilter_bbduk_windowsize = 50 + shortread_complexityfilter_bbduk_mask = false + // MALT run_malt = false malt_mode = 'BlastN' diff --git a/nextflow_schema.json b/nextflow_schema.json index fb2ca31..bd8b438 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -266,8 +266,7 @@ "type": "boolean" }, "shortread_clipmerge_excludeunmerged": { - "type": "boolean", - "default": false + "type": "boolean" }, "longread_clip": { "type": "boolean" @@ -304,6 +303,24 @@ "shortread_clipmerge_minlength": { "type": "integer", "default": 15 + }, + "shortread_complexityfilter_tool": { + "type": "string", + "default": "bbduk" + }, + "shortread_complexityfilter_bbduk_entropy": { + "type": "number", + "default": 0.3 + }, + "shortread_complexityfilter_bbduk_windowsize": { + "type": "integer", + "default": 50 + }, + "shortread_complexityfilter_bbduk_mask": { + "type": "boolean" + }, + "shortread_complexityfilter": { + "type": "boolean" } } } diff --git a/subworkflows/local/longread_preprocessing.nf b/subworkflows/local/longread_preprocessing.nf index a1515c7..2fa5f3b 100644 --- a/subworkflows/local/longread_preprocessing.nf +++ b/subworkflows/local/longread_preprocessing.nf @@ -1,6 +1,6 @@ -/* -Process long raw reads with porechop -*/ +// +// Process long raw reads with porechop +// include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main' include { PORECHOP } from '../../modules/nf-core/modules/porechop/main' @@ -25,7 +25,7 @@ workflow LONGREAD_PREPROCESSING { FASTQC_PROCESSED ( PORECHOP.out.reads ) ch_versions = ch_versions.mix(PORECHOP.out.versions.first()) - ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} ) + ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip ) emit: diff --git a/subworkflows/local/shortread_adapterremoval.nf b/subworkflows/local/shortread_adapterremoval.nf index 5e005db..b173e4c 100644 --- a/subworkflows/local/shortread_adapterremoval.nf +++ b/subworkflows/local/shortread_adapterremoval.nf @@ -1,6 +1,6 @@ -/* -Process short raw reads with AdapterRemoval -*/ +// +// 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' diff --git a/subworkflows/local/shortread_complexityfiltering.nf b/subworkflows/local/shortread_complexityfiltering.nf new file mode 100644 index 0000000..3d69ed6 --- /dev/null +++ b/subworkflows/local/shortread_complexityfiltering.nf @@ -0,0 +1,28 @@ +// +// Check input samplesheet and get read channels +// + +include { BBMAP_BBDUK } from '../../modules/nf-core/modules/bbmap/bbduk/main' + +workflow SHORTREAD_COMPLEXITYFILTERING { + take: + reads // [ [ meta ], [ reads ] ] + + main: + ch_versions = Channel.empty() + ch_multiqc_files = Channel.empty() + + if ( params.shortread_complexityfilter_tool == 'bbduk' ) { + ch_filtered_reads = BBMAP_BBDUK ( reads, [] ).reads + ch_versions = ch_versions.mix( BBMAP_BBDUK.out.versions.first() ) + ch_multiqc_files = ch_multiqc_files.mix( BBMAP_BBDUK.out.log ) + } else { + ch_filtered_reads = reads + } + + emit: + reads = ch_filtered_reads // channel: [ val(meta), [ reads ] ] + versions = ch_versions // channel: [ versions.yml ] + mqc = ch_multiqc_files +} + diff --git a/subworkflows/local/shortread_fastp.nf b/subworkflows/local/shortread_fastp.nf index 48817db..18baf17 100644 --- a/subworkflows/local/shortread_fastp.nf +++ b/subworkflows/local/shortread_fastp.nf @@ -1,6 +1,6 @@ -/* -Process short raw reads with FastP -*/ +// +// Process short raw reads with FastP +// include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main' include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main' @@ -44,8 +44,8 @@ workflow SHORTREAD_FASTP { 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 = ch_multiqc_files.mix( FASTP_SINGLE.out.json ) + ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json ) emit: reads = ch_processed_reads // channel: [ val(meta), [ reads ] ] diff --git a/subworkflows/local/shortread_preprocessing.nf b/subworkflows/local/shortread_preprocessing.nf index 1d0caac..b0ac25e 100644 --- a/subworkflows/local/shortread_preprocessing.nf +++ b/subworkflows/local/shortread_preprocessing.nf @@ -1,5 +1,5 @@ // -// Check input samplesheet and get read channels +// Perform read trimming and merging // @@ -9,7 +9,7 @@ include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules workflow SHORTREAD_PREPROCESSING { take: - reads // file: /path/to/samplesheet.csv + reads // [ [ meta ], [ reads ] ] main: ch_versions = Channel.empty() @@ -29,7 +29,7 @@ workflow SHORTREAD_PREPROCESSING { FASTQC_PROCESSED ( ch_processed_reads ) ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions ) - ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} ) + ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip ) emit: reads = ch_processed_reads // channel: [ val(meta), [ reads ] ] diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index ce89a91..a403589 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -40,9 +40,10 @@ 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 { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing' -include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing' +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_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -61,7 +62,6 @@ include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fas include { MALT_RUN } from '../modules/nf-core/modules/malt/run/main' include { KRAKEN2_KRAKEN2 } from '../modules/nf-core/modules/kraken2/kraken2/main' - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW @@ -98,10 +98,6 @@ workflow TAXPROFILER { ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) - /* SUBWORKFLOW: PERFORM PREPROCESSING */ @@ -114,17 +110,26 @@ 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_longreads_preprocessed = INPUT_CHECK.out.nanopore } + /* + SUBWORKFLOW: COMPLEXITY FILTERING + */ + + if ( params.shortread_complexityfilter ) { + ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads + } else { + ch_shortreads_filtered = 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], /2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], /malt90] - ch_input_for_profiling = ch_shortreads_preprocessed + ch_input_for_profiling = ch_shortreads_filtered .mix( ch_longreads_preprocessed ) .combine(DB_CHECK.out.dbs) .branch { @@ -177,6 +182,12 @@ workflow TAXPROFILER { /* MODULE: MultiQC */ + + CUSTOM_DUMPSOFTWAREVERSIONS ( + ch_versions.unique().collectFile(name: 'collated_versions.yml') + ) + + workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) @@ -188,21 +199,30 @@ workflow TAXPROFILER { ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) 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([])) - ch_versions = ch_versions.mix(KRAKEN2_KRAKEN2.out.versions.first()) - } - if (params.run_malt) { - ch_multiqc_files = ch_multiqc_files.mix(MALT_RUN.out.log.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(MALT_RUN.out.versions.first()) + ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_shortclipmerge") + ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions ) + } + + if (params.longread_clip) { + ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_longclipmerge") + ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions ) + } + + if (params.shortread_complexityfilter){ + ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_compelxity") + ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions ) + } + + if (params.run_kraken2) { + ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_kraken") + ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() ) + } + + if (params.run_malt) { + ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) ).dump(tag: "mqc_malt") + ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() ) } - // TODO MALT results overwriting per database? // TODO Versions for Karken/MALT not report? MULTIQC ( ch_multiqc_files.collect()