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Merge pull request #33 from nf-core/improve-shortread-input

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Improve shortread input preprocessing
This commit is contained in:
James A. Fellows Yates 2022-03-30 11:48:32 +02:00 committed by GitHub
commit 323883bd3e
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GPG key ID: 4AEE18F83AFDEB23
10 changed files with 173 additions and 131 deletions
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35
conf/modules.config
View file

@ -52,12 +52,27 @@ process {
]
}
withName: FASTQC_PROCESSED {
ext.args = '--quiet'
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
publishDir = [
path: { "${params.outdir}/fastqc/processed" },
mode: 'copy',
pattern: '*.html'
]
}
withName: FASTP {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
// TODO also include option to NOT merge
ext.args = [
{ ${meta.single_end} } == 0 ? "-m" : '',
params.shortread_excludeunmerged ? '' : "--include_unmerged"
// collapsing options - option to retain singletons
params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
// trimming options
params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
!{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
// filtering options
"--length_required ${params.shortread_clipmerge_minlength}"
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/fastp" },
@ -75,16 +90,6 @@ process {
]
}
withName: FASTQC_POST {
ext.args = '--quiet'
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
publishDir = [
path: { "${params.outdir}/fastqc/processed" },
mode: 'copy',
pattern: '*.html'
]
}
withName: CAT_FASTQ {
publishDir = [
path: { "${params.outdir}/prepared_sequences" },
@ -100,7 +105,7 @@ process {
pattern: '*.{rma6,tab,text,sam,log}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.db_name}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
withName: KRAKEN2_KRAKEN2 {
@ -110,7 +115,7 @@ process {
pattern: '*.{fastq.gz,txt}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = { "${meta.id}-${meta.db_name}" }
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
withName: CUSTOM_DUMPSOFTWAREVERSIONS {

1
conf/test.config
View file

@ -23,7 +23,6 @@ params {
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// 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'
outdir = "./results"
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
run_kraken2 = true
run_malt = true

6
modules.json
View file

@ -24,11 +24,11 @@
"multiqc": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"untar": {
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
},
"porechop": {
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
},
"untar": {
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
}
}
}

12
nextflow.config
View file

@ -55,9 +55,15 @@ params {
databases = null
// FASTQ preprocessing
shortread_clipmerge = false
shortread_excludeunmerged = true
longread_clip = false
shortread_clipmerge = false
shortread_clipmerge_tool = 'fastp'
shortread_clipmerge_skipadaptertrim = false
shortread_clipmerge_mergepairs = false
shortread_clipmerge_excludeunmerged = true
shortread_clipmerge_adapter1 = null
shortread_clipmerge_adapter2 = null
shortread_clipmerge_minlength = 15
longread_clip = false
// MALT
run_malt = false

24
nextflow_schema.json
View file

@ -265,7 +265,7 @@
"shortread_clipmerge": {
"type": "boolean"
},
"shortread_excludeunmerged": {
"shortread_clipmerge_excludeunmerged": {
"type": "boolean",
"default": true
},
@ -281,6 +281,28 @@
},
"run_kraken2": {
"type": "boolean"
},
"shortread_clipmerge_tool": {
"type": "string",
"default": "fastp"
},
"shortread_clipmerge_skipadaptertrim": {
"type": "boolean"
},
"shortread_clipmerge_mergepairs": {
"type": "boolean"
},
"shortread_clipmerge_adapter1": {
"type": "string",
"default": null
},
"shortread_clipmerge_adapter2": {
"type": "string",
"default": null
},
"shortread_clipmerge_minlength": {
"type": "integer",
"default": 15
}
}
}

5
subworkflows/local/db_check.nf
View file

@ -12,6 +12,9 @@ workflow DB_CHECK {
main:
// TODO: make database sheet check
// Checks:
// 1) no duplicates,
// 2) args do not have quotes, e.g. just `,,` and NOT `,"",`
parsed_samplesheet = DATABASE_CHECK ( dbsheet )
.csv
.splitCsv ( header:true, sep:',' )
@ -21,7 +24,7 @@ workflow DB_CHECK {
ch_dbs_for_untar = parsed_samplesheet
.branch {
untar: it[1].toString().endsWith(".tar.gz")
untar: it[1].toString().endsWith(".tar.gz") && it[0]['tool'] != 'centrifuge'
skip: true
}

11
subworkflows/local/longread_preprocessing.nf
View file

@ -1,6 +1,9 @@
/*
Process long raw reads with porechop
*/
include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
workflow LONGREAD_PREPROCESSING {
take:
@ -21,9 +24,9 @@ workflow LONGREAD_PREPROCESSING {
[ meta_new, reads ]
}
FASTQC_POST ( PORECHOP.out.reads )
FASTQC_PROCESSED ( 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]} )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} )
emit:

61
subworkflows/local/shortread_fastp.nf Normal file
View file

@ -0,0 +1,61 @@
/*
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'
workflow SHORTREAD_FASTP {
take:
reads // [[meta], [reads]]
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
ch_input_for_fastp = reads
.dump(tag: "pre-fastp_branch")
.branch{
single: it[0]['single_end'] == true
paired: it[0]['single_end'] == false
}
ch_input_for_fastp.single.dump(tag: "input_fastp_single")
ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
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 )
if ( params.shortread_clipmerge_mergepairs ) {
ch_fastp_reads_prepped_pe = FASTP_PAIRED.out.reads_merged
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )
} else {
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads
.mix( FASTP_SINGLE.out.reads )
}
ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
ch_processed_reads = ch_fastp_reads_prepped.dump(tag: "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.dump(tag: "preprocessing_fastp_mqc_final")
emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}

61
subworkflows/local/shortread_preprocessing.nf
View file

@ -3,67 +3,28 @@
//
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 { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
include { SHORTREAD_FASTP } from './shortread_fastp'
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
workflow SHORTREAD_PREPROCESSING {
take:
reads // file: /path/to/samplesheet.csv
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
//
// STEP: Read clipping and merging
//
// TODO give option to clip only and retain pairs
// TODO give option to retain singletons (probably fastp option likely)
// TODO move to subworkflow
if ( params.shortread_clipmerge ) {
ch_input_for_fastp = reads
.dump(tag: "pre-fastp_branch")
.branch{
single: it[0]['single_end'] == true
paired: it[0]['single_end'] == false
}
ch_input_for_fastp.single.dump(tag: "input_fastp_single")
ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
FASTP_PAIRED ( ch_input_for_fastp.paired, false, true )
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
.mix( FASTP_SINGLE.out.reads )
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
FASTQC_POST ( ch_fastp_reads_prepped )
ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
ch_processed_reads = ch_fastp_reads_prepped
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_POST.out.zip.collect{it[1]} )
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.dump(tag: "preprocessing_mqc_final")
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
if ( params.shortread_clipmerge_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 {
ch_processed_reads = reads
}
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]} )
emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]

88
workflows/taxprofiler.nf
View file

@ -17,6 +17,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
// Check mandatory parameters
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] warning: MALT does not except uncollapsed paired-reads. Pairs will be profiled as separate files."
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -36,11 +37,11 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
//
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
//
include { INPUT_CHECK } from '../subworkflows/local/input_check'
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 { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -73,9 +74,9 @@ workflow TAXPROFILER {
ch_versions = Channel.empty()
//
// SUBWORKFLOW: Read in samplesheet, validate and stage input files
//
/*
SUBWORKFLOW: Read in samplesheet, validate and stage input files
*/
INPUT_CHECK (
ch_input
)
@ -85,22 +86,24 @@ workflow TAXPROFILER {
ch_databases
)
//
// MODULE: Run FastQC
//
/*
MODULE: Run FastQC
*/
ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
FASTQC (
ch_input_for_fastqc
)
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
CUSTOM_DUMPSOFTWAREVERSIONS (
ch_versions.unique().collectFile(name: 'collated_versions.yml')
)
//
// PERFORM PREPROCESSING
//
/*
SUBWORKFLOW: PERFORM PREPROCESSING
*/
if ( params.shortread_clipmerge ) {
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
} else {
@ -115,53 +118,32 @@ workflow TAXPROFILER {
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
}
//
// PERFORM SHORT READ RUN MERGING
// TODO: Check not necessary for long reads too?
//
ch_processed_for_combine = ch_shortreads_preprocessed
.dump(tag: "prep_for_combine_grouping")
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['run_accession'] = 'combined'
[ meta_new, reads ]
}
.groupTuple ( by: 0 )
.branch{
combine: it[1].size() >= 2
skip: it[1].size() < 2
}
CAT_FASTQ ( ch_processed_for_combine.combine )
ch_reads_for_profiling = ch_processed_for_combine.skip
.dump(tag: "skip_combine")
.mix( CAT_FASTQ.out.reads )
.dump(tag: "files_for_profiling")
//
// 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]
ch_input_for_profiling = ch_reads_for_profiling
ch_input_for_profiling = ch_shortreads_preprocessed
.mix( ch_longreads_preprocessed )
.combine(DB_CHECK.out.dbs)
.dump(tag: "reads_plus_db")
.dump(tag: "reads_plus_db_clean")
.branch {
malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'] == 'kraken2'
unknown: true
}
//
// PREPARE PROFILER INPUT CHANNELS
//
/*
PREPARE PROFILER INPUT CHANNELS
*/
// We groupTuple to have all samples in one channel for MALT as database
// loading takes a long time, so we only want to run it once per database
// TODO document somewhere we only accept illumina short reads for MALT?
ch_input_for_malt = ch_input_for_profiling.malt
.dump(tag: "input_to_malt_prefilter")
.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
.dump(tag: "input_to_malt_postfilter")
.map {
it ->
def temp_meta = [ id: it[2]['db_name']] + it[2]
@ -169,7 +151,7 @@ workflow TAXPROFILER {
[ temp_meta, it[1], db ]
}
.groupTuple(by: [0,2])
.dump(tag: "input for malt")
.dump(tag: "input_to_malt")
.multiMap {
it ->
reads: [ it[0], it[1].flatten() ]
@ -178,16 +160,16 @@ workflow TAXPROFILER {
// We can run Kraken2 one-by-one sample-wise
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.dump(tag: "input for kraken")
.dump(tag: "input_to_kraken")
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
//
// RUN PROFILING
//
/*
MODULE: RUN PROFILING
*/
if ( params.run_malt ) {
MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
}
@ -196,9 +178,9 @@ workflow TAXPROFILER {
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
}
//
// MODULE: MultiQC
//
/*
MODULE: MultiQC
*/
workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
ch_workflow_summary = Channel.value(workflow_summary)