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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| // Import generic module functions | ||
| include { get_resources; initOptions; saveFiles } from '../../../lib/nf/functions' | ||
| RESOURCES = get_resources(workflow.profile, params.max_memory, params.max_cpus) | ||
| options = initOptions(params.containsKey("options") ? params.options : [:], 'bracken') | ||
| options.btype = options.btype ?: "tools" | ||
| conda_tools = "bioconda::bactopia-teton=1.0.0" | ||
| conda_name = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-") | ||
| conda_env = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools | ||
|
|
||
| process BRACKEN { | ||
| tag "$meta.id" | ||
| label 'process_high' | ||
|
|
||
| conda (params.enable_conda ? conda_env : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/bactopia-teton:1.0.0--hdfd78af_0' : | ||
| 'quay.io/biocontainers/bactopia-teton:1.0.0--hdfd78af_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(reads) | ||
| path db | ||
|
|
||
| output: | ||
| tuple val(meta), path("${prefix}.bracken.tsv") , emit: tsv | ||
| tuple val(meta), path('*classified*') , emit: classified | ||
| tuple val(meta), path('*unclassified*') , emit: unclassified | ||
| tuple val(meta), path("${prefix}.kraken2.report.txt"), emit: kraken2_report | ||
| tuple val(meta), path("${prefix}.bracken.report.txt"), emit: bracken_report | ||
| tuple val(meta), path("*.abundances.txt") , emit: abundances | ||
| tuple val(meta), path("*.krona.html") , emit: krona | ||
| path "*.{log,err}" , emit: logs, optional: true | ||
| path ".command.*" , emit: nf_logs | ||
| path "versions.yml", emit: versions | ||
|
|
||
| script: | ||
| prefix = options.suffix ? "${options.suffix}" : "${meta.id}" | ||
| def paired = meta.single_end ? "" : "--paired" | ||
| classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq" | ||
| unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq" | ||
| def is_tarball = db.getName().endsWith(".tar.gz") ? true : false | ||
| def BRACKEN_VERSION = "2.7" | ||
| def KRAKENTOOLS_VERSION = "1.2" | ||
| """ | ||
| if [ "$is_tarball" == "true" ]; then | ||
| mkdir database | ||
| tar -xzf $db -C database | ||
| KRAKEN_DB=\$(find database/ -name "hash.k2d" | sed 's=hash.k2d==') | ||
| else | ||
| KRAKEN_DB=\$(find $db/ -name "hash.k2d" | sed 's=hash.k2d==') | ||
| fi | ||
| kraken2 \\ | ||
| --db \$KRAKEN_DB \\ | ||
| --threads $task.cpus \\ | ||
| --unclassified-out $unclassified \\ | ||
| --classified-out $classified \\ | ||
| --report ${prefix}.kraken2.report.txt \\ | ||
| --gzip-compressed \\ | ||
| $paired \\ | ||
| $options.args \\ | ||
| $reads > kracken.out | ||
| # Get read length | ||
| if [ "${params.bracken_read_length}" == "0" ]; then | ||
| OBS_READ_LENGTH=\$(zcat ${reads[0]} | fastq-scan -q | jq -r '.qc_stats.read_median') | ||
| echo \$OBS_READ_LENGTH | ||
| # Pre-built Bracken databases come with 50,75,100,150,200,250,300, split the difference | ||
| if [ "\$OBS_READ_LENGTH" -gt 275 ]; then | ||
| READ_LENGTH="300" | ||
| elif [ "\$OBS_READ_LENGTH" -gt 225 ]; then | ||
| READ_LENGTH="250" | ||
| elif [ "\$OBS_READ_LENGTH" -gt 175 ]; then | ||
| READ_LENGTH="200" | ||
| elif [ "\$OBS_READ_LENGTH" -gt 125 ]; then | ||
| READ_LENGTH="150" | ||
| elif [ "\$OBS_READ_LENGTH" -gt 85 ]; then | ||
| READ_LENGTH="100" | ||
| elif [ "\$OBS_READ_LENGTH" -gt 65 ]; then | ||
| READ_LENGTH="75" | ||
| else | ||
| READ_LENGTH="50" | ||
| fi | ||
| else | ||
| # use user defined read length | ||
| READ_LENGTH="${params.bracken_read_length}" | ||
| fi | ||
| bracken \\ | ||
| $options.args2 \\ | ||
| -d \$KRAKEN_DB \\ | ||
| -r \$READ_LENGTH \\ | ||
| -i ${prefix}.kraken2.report.txt \\ | ||
| -w ${prefix}.bracken.report.txt \\ | ||
| -o bracken.temp | ||
| # Sort bracken report by 'fraction_total_reads' (column 7) | ||
| head -n 1 bracken.temp > ${prefix}.bracken.abundances.txt | ||
| grep -v "fraction_total_reads\$" bracken.temp | sort -k 7 -rn >> ${prefix}.bracken.abundances.txt | ||
| # Compress Kraken FASTQs | ||
| pigz -p $task.cpus *.fastq | ||
| # Adjust bracken to include unclassified and produce summary | ||
| kraken-bracken-summary.py \\ | ||
| ${prefix} \\ | ||
| ${prefix}.kraken2.report.txt \\ | ||
| ${prefix}.bracken.report.txt \\ | ||
| ${prefix}.bracken.abundances.txt | ||
| # Create a Krona report from reports | ||
| if [ "${params.skip_krona}" == "false" ]; then | ||
| # Kraken2 | ||
| kreport2krona.py \\ | ||
| --report ${prefix}.kraken2.report.txt \\ | ||
| --output kraken2-krona.temp | ||
| ktImportText -o ${prefix}.kraken2.krona.html kraken2-krona.temp | ||
| # Bracken | ||
| kreport2krona.py \\ | ||
| --report ${prefix}.bracken.report.txt \\ | ||
| --output bracken-krona.temp | ||
| ktImportText -o ${prefix}.bracken.krona.html bracken-krona.temp | ||
| rm *-krona.temp | ||
| fi | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| bracken: ${BRACKEN_VERSION} | ||
| fastq-scan: \$(echo \$(fastq-scan -v 2>&1) | sed 's/fastq-scan //') | ||
| jq: \$(echo \$(jq --version 2>&1) | sed 's/jq-//') | ||
| kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') | ||
| krakentools: ${KRAKENTOOLS_VERSION} | ||
| krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g') | ||
| pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) | ||
| python: \$(echo \$(python --version 2>&1) | sed 's/Python //') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| @@ -0,0 +1,60 @@ | ||
| name: kraken2 | ||
| description: Classifies metagenomic sequence data | ||
| keywords: | ||
| - classify | ||
| - metagenomics | ||
| - fastq | ||
| - db | ||
| tools: | ||
| - kraken2: | ||
| description: | | ||
| Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads | ||
| homepage: https://ccb.jhu.edu/software/kraken2/ | ||
| documentation: https://github.com/DerrickWood/kraken2/wiki/Manual | ||
| doi: 10.1186/s13059-019-1891-0 | ||
| licence: ['MIT'] | ||
| 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. | ||
| - db: | ||
| type: directory | ||
| description: Kraken2 database | ||
| output: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - classified: | ||
| type: file | ||
| description: | | ||
| Reads classified to belong to any of the taxa | ||
| on the Kraken2 database. | ||
| pattern: "*{fastq.gz}" | ||
| - unclassified: | ||
| type: file | ||
| description: | | ||
| Reads not classified to belong to any of the taxa | ||
| on the Kraken2 database. | ||
| pattern: "*{fastq.gz}" | ||
| - report: | ||
| type: file | ||
| description: | | ||
| Kraken2 report containing stats about classified | ||
| and not classifed reads. | ||
| pattern: "*.{report.txt}" | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| authors: | ||
| - "@joseespinosa" | ||
| - "@drpatelh" |
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|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| /* | ||
| This file includes default parameter values. | ||
| */ | ||
|
|
||
| params { | ||
| // Kraken2 | ||
| kraken2_db = null | ||
| kraken2_quick_mode = false | ||
| kraken2_confidence = 0.0 | ||
| kraken2_minimum_base_quality = 0 | ||
| kraken2_use_mpa_style = false | ||
| kraken2_report_zero_counts = false | ||
| kraken2_report_minimizer_data = false | ||
| kraken2_use_names = false | ||
| kraken2_memory_mapping = false | ||
| kraken2_minimum_hit_groups = 2 | ||
| bracken_read_length = 0 | ||
| bracken_level = "S" | ||
| bracken_threshold = 0 | ||
| skip_krona = false | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,117 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/kraken2/params.json", | ||
| "title": "Kraken2 Module", | ||
| "description": "A module for taxonomic classification of sequence reads", | ||
| "type": "object", | ||
| "definitions": { | ||
| "kraken2_bracken_parameters": { | ||
| "title": "Kraken2 and Bracken Parameters", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "fa_icon": "fas fa-exclamation-circle", | ||
| "properties": { | ||
| "kraken2_db": { | ||
| "type": "string", | ||
| "description": "The a single tarball or path to a Kraken2 formatted database", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "is_required": true | ||
| }, | ||
| "kraken2_quick_mode": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Quick operation (use first hit or hits)", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "kraken2_confidence": { | ||
| "type": "number", | ||
| "default": 0.0, | ||
| "description": "Confidence score threshold between 0 and 1", | ||
| "fa_icon": "fas fa-expand-arrows-alt" | ||
| }, | ||
| "kraken2_minimum_base_quality": { | ||
| "type": "integer", | ||
| "default": 0, | ||
| "description": "Minimum base quality used in classification", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "kraken2_use_mpa_style": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Format report output like Kraken 1's kraken-mpa-report", | ||
| "fa_icon": "fas fa-expand-arrows-alt" | ||
| }, | ||
| "kraken2_report_zero_counts": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Report counts for ALL taxa, even if counts are zero", | ||
| "fa_icon": "fas fa-expand-arrows-alt" | ||
| }, | ||
| "kraken2_report_minimizer_data": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Include minimizer and distinct minimizer count information in report", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "kraken2_use_names": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Print scientific names instead of just taxids", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "kraken2_memory_mapping": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Avoid loading database into RAM", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "kraken2_minimum_hit_groups": { | ||
| "type": "integer", | ||
| "default": 2, | ||
| "description": "Minimum number of hit groups needed to make a call", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "bracken_read_length": { | ||
| "type": "integer", | ||
| "default": 0, | ||
| "description": "Read length to get all classifications for (0 = determine at runtime)", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "bracken_level": { | ||
| "type": "string", | ||
| "default": "S", | ||
| "description": "Level to estimate abundance at", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "bracken_threshold": { | ||
| "type": "integer", | ||
| "default": 0, | ||
| "description": "Reads required PRIOR to abundance estimation to perform re-estimation", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| "skip_krona": { | ||
| "type": "boolean", | ||
| "default": false, | ||
| "description": "Skip the creation of a Krona report", | ||
| "fa_icon": "fas fa-expand-arrows-alt", | ||
| "hidden": true | ||
| }, | ||
| } | ||
| } | ||
| }, | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/kraken2_bracken_parameters" | ||
| } | ||
| ] | ||
| } |
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