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Add read improved read preprocessing

This commit is contained in:
James Fellows Yates 2022-03-25 14:58:06 +01:00
parent fafb7e0f6f
commit 4e93abc7c0
6 changed files with 107 additions and 50 deletions

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
params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
// trimming options
params.shortread_clipmerge_skiptrim ? "--disable_adapter_trimming" : "",
params.shortread_adapter1 ? "--adapter_sequence ${params.shortread_adapter1}" : "",
!{ ${meta.single_end} } && params.shortread_adapter2 ? "--adapter_sequence_r2 ${params.shortread_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : ""
// filtering options
"--length_required ${params.shortread_clipmerge_minlength}"
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/fastp" },

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_skiptrim = 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

View file

@ -265,7 +265,7 @@
"shortread_clipmerge": {
"type": "boolean"
},
"shortread_excludeunmerged": {
"shortread_clipmerge_excludeunmerged": {
"type": "boolean",
"default": true
},

View file

@ -0,0 +1,65 @@
//
// Check input samplesheet and get read channels
//
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 // file: /path/to/samplesheet.csv
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
//
// STEP: Read clipping and merging
//
// TODO give option to retain singletons (probably fastp option likely)
// TODO move to subworkflow
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, params.shortread_clipmerge_mergepairs )
if ( params.shortread_clipmerge_mergepairs ) {
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 ]
}
} 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
}

View file

@ -3,17 +3,16 @@
//
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()
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
//
// STEP: Read clipping and merging
@ -22,50 +21,20 @@ workflow SHORTREAD_PREPROCESSING {
// 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")
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:
// TODO: problem, this is being exported as a multi-channel output? This is why FASTQC is broken
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files

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."
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -135,6 +136,7 @@ workflow TAXPROFILER {
CAT_FASTQ ( ch_processed_for_combine.combine )
// TODO May need to flatten reads?
ch_reads_for_profiling = ch_processed_for_combine.skip
.dump(tag: "skip_combine")
.mix( CAT_FASTQ.out.reads )