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Add bbduk complexity (entropy-based) filtering

This commit is contained in:
James Fellows Yates 2022-04-02 17:02:05 +02:00
parent 1dfbcacf68
commit b055df5ea0
13 changed files with 222 additions and 45 deletions

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@ -26,6 +26,8 @@
- [Porechop](https://github.com/rrwick/Porechop) - [Porechop](https://github.com/rrwick/Porechop)
- [BBTools](http://sourceforge.net/projects/bbmap/)
- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0) - [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. > 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.

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@ -132,7 +132,6 @@ process {
] ]
} }
withName: PORECHOP { withName: PORECHOP {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ 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 = [ publishDir = [
path: { "${params.outdir}/prepared_sequences" }, path: { "${params.outdir}/bbduk/" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.{fastq.gz,log}'
] ]
} }

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@ -6,6 +6,9 @@
"adapterremoval": { "adapterremoval": {
"git_sha": "f0800157544a82ae222931764483331a81812012" "git_sha": "f0800157544a82ae222931764483331a81812012"
}, },
"bbmap/bbduk": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"cat/fastq": { "cat/fastq": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}, },

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@ -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
"""
}

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@ -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"

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@ -65,6 +65,13 @@ params {
shortread_clipmerge_minlength = 15 shortread_clipmerge_minlength = 15
longread_clip = false 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 // MALT
run_malt = false run_malt = false
malt_mode = 'BlastN' malt_mode = 'BlastN'

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@ -266,8 +266,7 @@
"type": "boolean" "type": "boolean"
}, },
"shortread_clipmerge_excludeunmerged": { "shortread_clipmerge_excludeunmerged": {
"type": "boolean", "type": "boolean"
"default": false
}, },
"longread_clip": { "longread_clip": {
"type": "boolean" "type": "boolean"
@ -304,6 +303,24 @@
"shortread_clipmerge_minlength": { "shortread_clipmerge_minlength": {
"type": "integer", "type": "integer",
"default": 15 "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"
} }
} }
} }

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@ -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 { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/modules/porechop/main' include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
@ -25,7 +25,7 @@ workflow LONGREAD_PREPROCESSING {
FASTQC_PROCESSED ( PORECHOP.out.reads ) FASTQC_PROCESSED ( PORECHOP.out.reads )
ch_versions = ch_versions.mix(PORECHOP.out.versions.first()) 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: emit:

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@ -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_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main'
include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main' include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'

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@ -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
}

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@ -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_SINGLE } from '../../modules/nf-core/modules/fastp/main'
include { FASTP as FASTP_PAIRED } 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_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_SINGLE.out.json )
ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} ) ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json )
emit: emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ] reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]

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@ -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 { workflow SHORTREAD_PREPROCESSING {
take: take:
reads // file: /path/to/samplesheet.csv reads // [ [ meta ], [ reads ] ]
main: main:
ch_versions = Channel.empty() ch_versions = Channel.empty()
@ -29,7 +29,7 @@ workflow SHORTREAD_PREPROCESSING {
FASTQC_PROCESSED ( ch_processed_reads ) FASTQC_PROCESSED ( ch_processed_reads )
ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions ) 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: emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ] reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]

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@ -43,6 +43,7 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { DB_CHECK } from '../subworkflows/local/db_check' include { DB_CHECK } from '../subworkflows/local/db_check'
include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing' include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_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 { MALT_RUN } from '../modules/nf-core/modules/malt/run/main'
include { KRAKEN2_KRAKEN2 } from '../modules/nf-core/modules/kraken2/kraken2/main' include { KRAKEN2_KRAKEN2 } from '../modules/nf-core/modules/kraken2/kraken2/main'
/* /*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW RUN MAIN WORKFLOW
@ -98,10 +98,6 @@ workflow TAXPROFILER {
ch_versions = ch_versions.mix(FASTQC.out.versions.first()) ch_versions = ch_versions.mix(FASTQC.out.versions.first())
CUSTOM_DUMPSOFTWAREVERSIONS (
ch_versions.unique().collectFile(name: 'collated_versions.yml')
)
/* /*
SUBWORKFLOW: PERFORM PREPROCESSING SUBWORKFLOW: PERFORM PREPROCESSING
*/ */
@ -114,17 +110,26 @@ workflow TAXPROFILER {
if ( params.longread_clip ) { if ( params.longread_clip ) {
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
.map { it -> [ it[0], [it[1]] ] } .map { it -> [ it[0], [it[1]] ] }
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
} else { } else {
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore 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 COMBINE READS WITH POSSIBLE DATABASES
*/ */
// e.g. 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] // e.g. 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_shortreads_preprocessed ch_input_for_profiling = ch_shortreads_filtered
.mix( ch_longreads_preprocessed ) .mix( ch_longreads_preprocessed )
.combine(DB_CHECK.out.dbs) .combine(DB_CHECK.out.dbs)
.branch { .branch {
@ -177,6 +182,12 @@ workflow TAXPROFILER {
/* /*
MODULE: MultiQC MODULE: MultiQC
*/ */
CUSTOM_DUMPSOFTWAREVERSIONS (
ch_versions.unique().collectFile(name: 'collated_versions.yml')
)
workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params) workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
ch_workflow_summary = Channel.value(workflow_summary) 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([])) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
if (params.shortread_clipmerge) { if (params.shortread_clipmerge) {
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.mqc) 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) { if (params.longread_clip) {
ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc) 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) { if (params.run_kraken2) {
ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([])) 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() ) ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
} }
if (params.run_malt) { if (params.run_malt) {
ch_multiqc_files = ch_multiqc_files.mix(MALT_RUN.out.log.collect{it[1]}.ifEmpty([])) 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() ) ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() )
} }
// TODO MALT results overwriting per database?
// TODO Versions for Karken/MALT not report? // TODO Versions for Karken/MALT not report?
MULTIQC ( MULTIQC (
ch_multiqc_files.collect() ch_multiqc_files.collect()