mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 07:43:08 +00:00
Merge pull request #33 from nf-core/improve-shortread-input
Improve shortread input preprocessing
This commit is contained in:
commit
323883bd3e
10 changed files with 173 additions and 131 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 - option to retain singletons
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params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
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// trimming options
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params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
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!{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_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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@ -75,16 +90,6 @@ process {
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]
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}
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withName: FASTQC_POST {
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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: { "${params.outdir}/fastqc/processed" },
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mode: 'copy',
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pattern: '*.html'
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]
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}
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withName: CAT_FASTQ {
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publishDir = [
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path: { "${params.outdir}/prepared_sequences" },
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@ -100,7 +105,7 @@ process {
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pattern: '*.{rma6,tab,text,sam,log}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KRAKEN2_KRAKEN2 {
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@ -110,7 +115,7 @@ process {
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pattern: '*.{fastq.gz,txt}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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@ -23,7 +23,6 @@ params {
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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outdir = "./results"
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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run_kraken2 = true
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run_malt = true
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@ -24,11 +24,11 @@
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"multiqc": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"untar": {
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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},
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"porechop": {
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"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
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},
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"untar": {
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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}
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}
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}
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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_skipadaptertrim = 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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@ -281,6 +281,28 @@
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},
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"run_kraken2": {
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"type": "boolean"
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},
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp"
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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},
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"shortread_clipmerge_mergepairs": {
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"type": "boolean"
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},
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"shortread_clipmerge_adapter1": {
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"type": "string",
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"default": null
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},
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"shortread_clipmerge_adapter2": {
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"type": "string",
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"default": null
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},
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"shortread_clipmerge_minlength": {
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"type": "integer",
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"default": 15
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}
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}
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}
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@ -12,6 +12,9 @@ workflow DB_CHECK {
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main:
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// TODO: make database sheet check
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// Checks:
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// 1) no duplicates,
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// 2) args do not have quotes, e.g. just `,,` and NOT `,"",`
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parsed_samplesheet = DATABASE_CHECK ( dbsheet )
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.csv
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.splitCsv ( header:true, sep:',' )
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@ -21,7 +24,7 @@ workflow DB_CHECK {
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ch_dbs_for_untar = parsed_samplesheet
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.branch {
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untar: it[1].toString().endsWith(".tar.gz")
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untar: it[1].toString().endsWith(".tar.gz") && it[0]['tool'] != 'centrifuge'
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skip: true
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}
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@ -1,6 +1,9 @@
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/*
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Process long raw reads with porechop
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*/
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include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
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include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
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include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
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workflow LONGREAD_PREPROCESSING {
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take:
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@ -21,9 +24,9 @@ workflow LONGREAD_PREPROCESSING {
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[ meta_new, reads ]
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}
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FASTQC_POST ( PORECHOP.out.reads )
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FASTQC_PROCESSED ( PORECHOP.out.reads )
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ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
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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( FASTQC_PROCESSED.out.zip.collect{it[1]} )
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emit:
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61
subworkflows/local/shortread_fastp.nf
Normal file
61
subworkflows/local/shortread_fastp.nf
Normal file
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@ -0,0 +1,61 @@
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/*
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Process short raw reads with FastP
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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 // [[meta], [reads]]
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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_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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// Last parameter here turns on merging of PE data
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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_pe = FASTP_PAIRED.out.reads_merged
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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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ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )
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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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@ -3,67 +3,28 @@
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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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//
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// STEP: Read clipping and merging
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//
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// TODO give option to clip only and retain pairs
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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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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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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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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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|
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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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@ -36,11 +37,11 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
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//
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// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
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//
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include { INPUT_CHECK } from '../subworkflows/local/input_check'
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include { INPUT_CHECK } from '../subworkflows/local/input_check'
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include { DB_CHECK } from '../subworkflows/local/db_check'
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include { DB_CHECK } from '../subworkflows/local/db_check'
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include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
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include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
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include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
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/*
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||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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|
@ -73,9 +74,9 @@ workflow TAXPROFILER {
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ch_versions = Channel.empty()
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//
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// SUBWORKFLOW: Read in samplesheet, validate and stage input files
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||||
//
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||||
/*
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SUBWORKFLOW: Read in samplesheet, validate and stage input files
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||||
*/
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INPUT_CHECK (
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ch_input
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)
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|
@ -85,22 +86,24 @@ workflow TAXPROFILER {
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ch_databases
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)
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//
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// MODULE: Run FastQC
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||||
//
|
||||
/*
|
||||
MODULE: Run FastQC
|
||||
*/
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||||
ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
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||||
|
||||
FASTQC (
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ch_input_for_fastqc
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||||
)
|
||||
|
||||
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
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||||
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||||
CUSTOM_DUMPSOFTWAREVERSIONS (
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ch_versions.unique().collectFile(name: 'collated_versions.yml')
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)
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||||
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||||
//
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||||
// PERFORM PREPROCESSING
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||||
//
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||||
/*
|
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SUBWORKFLOW: PERFORM PREPROCESSING
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*/
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if ( params.shortread_clipmerge ) {
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ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
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} else {
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|
@ -115,53 +118,32 @@ workflow TAXPROFILER {
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ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
|
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}
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|
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//
|
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// PERFORM SHORT READ RUN MERGING
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// TODO: Check not necessary for long reads too?
|
||||
//
|
||||
ch_processed_for_combine = ch_shortreads_preprocessed
|
||||
.dump(tag: "prep_for_combine_grouping")
|
||||
.map {
|
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meta, reads ->
|
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def meta_new = meta.clone()
|
||||
meta_new['run_accession'] = 'combined'
|
||||
[ meta_new, reads ]
|
||||
}
|
||||
.groupTuple ( by: 0 )
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||||
.branch{
|
||||
combine: it[1].size() >= 2
|
||||
skip: it[1].size() < 2
|
||||
}
|
||||
|
||||
CAT_FASTQ ( ch_processed_for_combine.combine )
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||||
|
||||
ch_reads_for_profiling = ch_processed_for_combine.skip
|
||||
.dump(tag: "skip_combine")
|
||||
.mix( CAT_FASTQ.out.reads )
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||||
.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)
|
||||
|
||||
|
|
Loading…
Reference in a new issue