mirror of
https://github.com/MillironX/taxprofiler.git
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332 lines
15 KiB
Text
332 lines
15 KiB
Text
/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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VALIDATE INPUTS
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
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// Validate input parameters
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WorkflowTaxprofiler.initialise(params, log)
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// TODO nf-core: Add all file path parameters for the pipeline to the list below
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// Check input path parameters to see if they exist
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def checkPathParamList = [ params.input, params.databases, params.hostremoval_reference,
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params.shortread_hostremoval_index, params.multiqc_config,
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params.shortread_qc_adapterlist
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]
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for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
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// Check mandatory parameters
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if ( params.input ) {
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ch_input = file(params.input, checkIfExists: true)
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pep_input_base_dir = file(params.input).extension.matches("yaml|yml") ? file(file(params.input).getParent(), checkIfExists: true) : []
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} else {
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exit 1, "Input samplesheet, or PEP config and base directory not specified"
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}
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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_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs"
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if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' )) exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"
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if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input." }
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if (!params.hostremoval_reference && params.hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
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if (params.hostremoval_reference ) { ch_reference = file(params.hostremoval_reference) }
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if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] }
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if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] }
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if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available."
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if (params.run_malt && params.run_krona && !params.krona_taxonomy_directory) log.warn "[nf-core/taxprofiler] Krona can only be run on MALT output if path to Krona taxonomy database supplied to --krona_taxonomy_directory. Krona will not be executed in this run for MALT."
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if (params.run_bracken && !params.run_kraken2) exit 1, 'ERROR: [nf-core/taxprofiler] You are attempting to run Bracken without running kraken2. This is not possible! Please set --run_kraken2 as well.'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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CONFIG FILES
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
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ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
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ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
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ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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IMPORT LOCAL MODULES/SUBWORKFLOWS
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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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 { 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 { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_hostremoval'
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include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_hostremoval'
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include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
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include { PROFILING } from '../subworkflows/local/profiling'
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include { VISUALIZATION_KRONA } from '../subworkflows/local/visualization_krona'
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include { STANDARDISATION_PROFILES } from '../subworkflows/local/standardisation_profiles'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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IMPORT NF-CORE MODULES/SUBWORKFLOWS
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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//
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// MODULE: Installed directly from nf-core/modules
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//
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include { FASTQC } from '../modules/nf-core/fastqc/main'
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include { FALCO } from '../modules/nf-core/falco/main'
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include { MULTIQC } from '../modules/nf-core/multiqc/main'
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include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
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include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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RUN MAIN WORKFLOW
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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// Info required for completion email and summary
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def multiqc_report = []
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workflow TAXPROFILER {
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ch_versions = Channel.empty()
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ch_multiqc_logo= Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")
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adapterlist = params.shortread_qc_adapterlist ? file(params.shortread_qc_adapterlist) : []
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if ( params.shortread_qc_adapterlist ) {
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if ( params.shortread_qc_tool == 'adapterremoval' && !(adapterlist.extension == 'txt') ) error "[nf-core/taxprofiler] ERROR: AdapterRemoval2 adapter list requires a `.txt` format and extension. Check input: --shortread_qc_adapterlist ${params.shortread_qc_adapterlist}"
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if ( params.shortread_qc_tool == 'fastp' && !adapterlist.extension.matches(".*(fa|fasta|fna|fas)") ) error "[nf-core/taxprofiler] ERROR: fastp adapter list requires a `.fasta` format and extension (or fa, fas, fna). Check input: --shortread_qc_adapterlist ${params.shortread_qc_adapterlist}"
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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, pep_input_base_dir
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)
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ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
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DB_CHECK (
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ch_databases
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)
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ch_versions = ch_versions.mix(DB_CHECK.out.versions)
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/*
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MODULE: Run FastQC
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*/
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ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
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if ( params.preprocessing_qc_tool == 'falco' ) {
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FALCO ( ch_input_for_fastqc )
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ch_versions = ch_versions.mix(FALCO.out.versions.first())
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} else {
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FASTQC ( 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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/*
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SUBWORKFLOW: PERFORM PREPROCESSING
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*/
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if ( params.perform_shortread_qc ) {
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ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq, adapterlist ).reads
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ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
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} else {
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ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
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}
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if ( params.perform_longread_qc ) {
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ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
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.map { it -> [ it[0], [it[1]] ] }
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ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
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} else {
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ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
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}
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/*
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SUBWORKFLOW: COMPLEXITY FILTERING
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*/
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// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
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if ( params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp' ) {
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ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
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ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
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} else {
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ch_shortreads_filtered = ch_shortreads_preprocessed
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}
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/*
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SUBWORKFLOW: HOST REMOVAL
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*/
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if ( params.perform_shortread_hostremoval ) {
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ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_shortread_reference_index ).reads
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ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
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} else {
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ch_shortreads_hostremoved = ch_shortreads_filtered
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}
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if ( params.perform_longread_hostremoval ) {
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ch_longreads_hostremoved = LONGREAD_HOSTREMOVAL ( ch_longreads_preprocessed, ch_reference, ch_longread_reference_index ).reads
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ch_versions = ch_versions.mix(LONGREAD_HOSTREMOVAL.out.versions)
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} else {
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ch_longreads_hostremoved = ch_longreads_preprocessed
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}
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if ( params.perform_runmerging ) {
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ch_reads_for_cat_branch = ch_shortreads_hostremoved
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.mix( ch_longreads_hostremoved )
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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.remove('run_accession')
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[ meta_new, reads ]
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}
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.groupTuple()
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.map {
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meta, reads ->
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[ meta, reads.flatten() ]
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}
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.branch {
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meta, reads ->
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// we can't concatenate files if there is not a second run, we branch
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// here to separate them out, and mix back in after for efficiency
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cat: ( meta.single_end && reads.size() > 1 ) || ( !meta.single_end && reads.size() > 2 )
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skip: true
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}
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ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat_branch.cat ).reads
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.mix( ch_reads_for_cat_branch.skip )
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.map {
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meta, reads ->
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[ meta, [ reads ].flatten() ]
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}
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.mix( INPUT_CHECK.out.fasta )
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ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
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} else {
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ch_reads_runmerged = ch_shortreads_hostremoved
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.mix( ch_longreads_hostremoved, INPUT_CHECK.out.fasta )
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}
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/*
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SUBWORKFLOW: PROFILING
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*/
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PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
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ch_versions = ch_versions.mix( PROFILING.out.versions )
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/*
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SUBWORKFLOW: VISUALIZATION_KRONA
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*/
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if ( params.run_krona ) {
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VISUALIZATION_KRONA ( PROFILING.out.classifications, PROFILING.out.profiles, DB_CHECK.out.dbs )
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ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
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}
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/*
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SUBWORKFLOW: PROFILING STANDARDISATION
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*/
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if ( params.run_profile_standardisation ) {
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STANDARDISATION_PROFILES ( PROFILING.out.classifications, PROFILING.out.profiles, DB_CHECK.out.dbs, PROFILING.out.motus_version )
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ch_versions = ch_versions.mix( STANDARDISATION_PROFILES.out.versions )
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}
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/*
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MODULE: MultiQC
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*/
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CUSTOM_DUMPSOFTWAREVERSIONS (
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ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml')
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)
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workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
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ch_workflow_summary = Channel.value(workflow_summary)
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methods_description = WorkflowTaxprofiler.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
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ch_methods_description = Channel.value(methods_description)
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ch_multiqc_files = Channel.empty()
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ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
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ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
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ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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if ( params.preprocessing_qc_tool == 'falco' ) {
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ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect{it[1]}.ifEmpty([]))
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} else {
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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}
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if (params.perform_shortread_qc) {
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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}
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if (params.perform_longread_qc) {
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ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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}
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if (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp'){
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
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}
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if (params.perform_shortread_hostremoval) {
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ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
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}
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if (params.perform_longread_hostremoval) {
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ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
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}
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ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc.collect{it[1]}.ifEmpty([]) )
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if ( params.run_profile_standardisation ) {
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ch_multiqc_files = ch_multiqc_files.mix( STANDARDISATION_PROFILES.out.mqc.collect{it[1]}.ifEmpty([]) )
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}
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// TODO create multiQC module for metaphlan
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MULTIQC (
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ch_multiqc_files.collect(),
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ch_multiqc_config.toList(),
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ch_multiqc_custom_config.toList(),
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ch_multiqc_logo.toList()
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)
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multiqc_report = MULTIQC.out.report.toList()
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}
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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COMPLETION EMAIL AND SUMMARY
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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workflow.onComplete {
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if (params.email || params.email_on_fail) {
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NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
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}
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NfcoreTemplate.summary(workflow, params, log)
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if (params.hook_url) {
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NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
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}
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}
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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THE END
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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