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https://github.com/MillironX/taxprofiler.git
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Add read improved read preprocessing
This commit is contained in:
James Fellows Yates
parent
fafb7e0f6f
commit
4e93abc7c0
6 changed files with 107 additions and 50 deletions
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@ -52,12 +52,27 @@ process {
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]
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}
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withName: FASTQC_PROCESSED {
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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publishDir = [
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path: { "${params.outdir}/fastqc/processed" },
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mode: 'copy',
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pattern: '*.html'
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]
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}
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withName: FASTP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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// TODO also include option to NOT merge
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ext.args = [
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{ ${meta.single_end} } == 0 ? "-m" : '',
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params.shortread_excludeunmerged ? '' : "--include_unmerged"
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// collapsing options
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params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
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// trimming options
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params.shortread_clipmerge_skiptrim ? "--disable_adapter_trimming" : "",
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params.shortread_adapter1 ? "--adapter_sequence ${params.shortread_adapter1}" : "",
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!{ ${meta.single_end} } && params.shortread_adapter2 ? "--adapter_sequence_r2 ${params.shortread_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : ""
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}"
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].join(' ').trim()
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publishDir = [
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path: { "${params.outdir}/fastp" },
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@ -55,9 +55,15 @@ params {
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databases = null
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// FASTQ preprocessing
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shortread_clipmerge = false
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shortread_excludeunmerged = true
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longread_clip = false
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shortread_clipmerge = false
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shortread_clipmerge_tool = 'fastp'
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shortread_clipmerge_skiptrim = false
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shortread_clipmerge_mergepairs = false
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shortread_clipmerge_excludeunmerged = true
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shortread_clipmerge_adapter1 = null
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shortread_clipmerge_adapter2 = null
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shortread_clipmerge_minlength = 15
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longread_clip = false
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// MALT
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run_malt = false
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@ -265,7 +265,7 @@
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"shortread_clipmerge": {
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"type": "boolean"
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},
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"shortread_excludeunmerged": {
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"shortread_clipmerge_excludeunmerged": {
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"type": "boolean",
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"default": true
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},
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65
subworkflows/local/shortread_fastp.nf
Normal file
65
subworkflows/local/shortread_fastp.nf
Normal file
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@ -0,0 +1,65 @@
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//
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// Check input samplesheet and get read channels
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//
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include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
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include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
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workflow SHORTREAD_FASTP {
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take:
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reads // file: /path/to/samplesheet.csv
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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//
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// STEP: Read clipping and merging
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//
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// TODO give option to retain singletons (probably fastp option likely)
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// TODO move to subworkflow
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ch_input_for_fastp = reads
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.dump(tag: "pre-fastp_branch")
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.branch{
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single: it[0]['single_end'] == true
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paired: it[0]['single_end'] == false
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}
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ch_input_for_fastp.single.dump(tag: "input_fastp_single")
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ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
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FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
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FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_clipmerge_mergepairs )
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if ( params.shortread_clipmerge_mergepairs ) {
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ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
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.mix( FASTP_SINGLE.out.reads )
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['single_end'] = 1
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[ meta_new, reads ]
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}
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} else {
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ch_fastp_reads_prepped = FASTP_PAIRED.out.reads
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.mix( FASTP_SINGLE.out.reads )
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}
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ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
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ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
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ch_processed_reads = ch_fastp_reads_prepped.dump(tag: "ch_fastp_reads_prepped")
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json.collect{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} )
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ch_multiqc_files.dump(tag: "preprocessing_fastp_mqc_final")
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emit:
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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@ -3,17 +3,16 @@
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//
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include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
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include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
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include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
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include { SHORTREAD_FASTP } from './shortread_fastp'
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
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workflow SHORTREAD_PREPROCESSING {
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take:
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reads // file: /path/to/samplesheet.csv
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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//
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// STEP: Read clipping and merging
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@ -22,50 +21,20 @@ workflow SHORTREAD_PREPROCESSING {
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// TODO give option to retain singletons (probably fastp option likely)
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// TODO move to subworkflow
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if ( params.shortread_clipmerge ) {
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ch_input_for_fastp = reads
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.dump(tag: "pre-fastp_branch")
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.branch{
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single: it[0]['single_end'] == true
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paired: it[0]['single_end'] == false
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}
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ch_input_for_fastp.single.dump(tag: "input_fastp_single")
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ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
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FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
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FASTP_PAIRED ( ch_input_for_fastp.paired, false, true )
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ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
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.mix( FASTP_SINGLE.out.reads )
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['single_end'] = 1
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[ meta_new, reads ]
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}
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FASTQC_POST ( ch_fastp_reads_prepped )
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ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
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ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
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ch_processed_reads = ch_fastp_reads_prepped
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ch_multiqc_files = ch_multiqc_files.mix( FASTQC_POST.out.zip.collect{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json.collect{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} )
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ch_multiqc_files.dump(tag: "preprocessing_mqc_final")
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if ( params.shortread_clipmerge_tool == "fastp" ) {
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ch_processed_reads = SHORTREAD_FASTP ( reads ).reads
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ch_versions = ch_versions.mix( SHORTREAD_FASTP.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
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} else {
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ch_processed_reads = reads
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}
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//FASTQC_PROCESSED ( ch_processed_reads )
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//ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
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//ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} )
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emit:
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// TODO: problem, this is being exported as a multi-channel output? This is why FASTQC is broken
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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@ -17,6 +17,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
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// Check mandatory parameters
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if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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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."
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -135,6 +136,7 @@ workflow TAXPROFILER {
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CAT_FASTQ ( ch_processed_for_combine.combine )
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// TODO May need to flatten reads?
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ch_reads_for_profiling = ch_processed_for_combine.skip
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.dump(tag: "skip_combine")
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.mix( CAT_FASTQ.out.reads )
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