mirror of
https://github.com/MillironX/taxprofiler.git
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264 lines
10 KiB
Text
264 lines
10 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.shortread_hostremoval_reference,
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params.shortread_hostremoval_index, params.multiqc_config
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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 ) { 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 accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
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// TODO Add check if index but no reference exit 1
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if (params.shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) } else { ch_reference = [] }
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if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
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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 = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
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ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
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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 { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
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include { PROFILING } from '../subworkflows/local/profiling'
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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/modules/fastqc/main'
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include { MULTIQC } from '../modules/nf-core/modules/multiqc/main'
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include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
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include { CAT_FASTQ } from '../modules/nf-core/modules/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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/*
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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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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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FASTQC (
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ch_input_for_fastqc
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)
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ch_versions = ch_versions.mix(FASTQC.out.versions.first())
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/*
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SUBWORKFLOW: PERFORM PREPROCESSING
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*/
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if ( params.perform_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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ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
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}
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if ( params.perform_longread_clip ) {
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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.first())
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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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if ( params.perform_shortread_complexityfilter ) {
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ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
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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.shortread_hostremoval ) {
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ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
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ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
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} else {
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ch_shortreads_hostremoved = ch_shortreads_filtered
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}
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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_preprocessed )
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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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} else {
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ch_reads_runmerged = ch_shortreads_hostremoved
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.mix( ch_longreads_preprocessed )
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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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MODULE: MultiQC
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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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workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
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ch_workflow_summary = Channel.value(workflow_summary)
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ch_multiqc_files = Channel.empty()
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ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
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ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
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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(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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if (params.perform_shortread_clipmerge) {
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
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}
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if (params.perform_longread_clip) {
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ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
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}
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if (params.perform_shortread_complexityfilter){
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
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ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
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}
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if (params.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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ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
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}
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if (params.perform_runmerging){
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ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
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}
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ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )
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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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)
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multiqc_report = MULTIQC.out.report.toList()
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ch_versions = ch_versions.mix(MULTIQC.out.versions)
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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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}
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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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