mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-23 15:19:55 +00:00
342 lines
16 KiB
Text
342 lines
16 KiB
Text
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
VALIDATE INPUTS
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
|
|
|
|
// Validate input parameters
|
|
WorkflowTaxprofiler.initialise(params, log)
|
|
|
|
// Check input path parameters to see if they exist
|
|
def checkPathParamList = [ params.input, params.genome, params.databases,
|
|
params.outdir, params.longread_hostremoval_index,
|
|
params.hostremoval_reference, params.shortread_hostremoval_index,
|
|
params.multiqc_config, params.shortread_qc_adapterlist,
|
|
params.krona_taxonomy_directory,
|
|
params.taxpasta_taxonomy_dir,
|
|
params.multiqc_logo, params.multiqc_methods_description
|
|
]
|
|
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
|
|
|
|
// Check mandatory parameters
|
|
if ( params.input ) {
|
|
ch_input = file(params.input, checkIfExists: true)
|
|
} else {
|
|
error("Input samplesheet not specified")
|
|
}
|
|
|
|
if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { error('Input database sheet not specified!') }
|
|
|
|
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."
|
|
if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) error("ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs")
|
|
|
|
if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' )) error("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'")
|
|
|
|
if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { error("ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input.") }
|
|
if (params.perform_shortread_hostremoval && !params.hostremoval_reference && params.shortread_hostremoval_index) { error("ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input.") }
|
|
if (params.perform_longread_hostremoval && !params.hostremoval_reference && params.longread_hostremoval_index) { error("ERROR: [nf-core/taxprofiler] --longread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input.") }
|
|
|
|
if (params.hostremoval_reference ) { ch_reference = file(params.hostremoval_reference) }
|
|
if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = Channel.fromPath(params.shortread_hostremoval_index).map{[[], it]} } else { ch_shortread_reference_index = [] }
|
|
if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] }
|
|
|
|
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."
|
|
|
|
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."
|
|
if (params.run_bracken && !params.run_kraken2) error('ERROR: [nf-core/taxprofiler] You are attempting to run Bracken without running kraken2. This is not possible! Please set --run_kraken2 as well.')
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
CONFIG FILES
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
|
|
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
|
|
ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
|
|
ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
IMPORT LOCAL MODULES/SUBWORKFLOWS
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
//
|
|
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
|
|
//
|
|
include { INPUT_CHECK } from '../subworkflows/local/input_check'
|
|
|
|
include { DB_CHECK } from '../subworkflows/local/db_check'
|
|
include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
|
|
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
|
|
include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_hostremoval'
|
|
include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_hostremoval'
|
|
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
|
|
include { PROFILING } from '../subworkflows/local/profiling'
|
|
include { VISUALIZATION_KRONA } from '../subworkflows/local/visualization_krona'
|
|
include { STANDARDISATION_PROFILES } from '../subworkflows/local/standardisation_profiles'
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
IMPORT NF-CORE MODULES/SUBWORKFLOWS
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
//
|
|
// MODULE: Installed directly from nf-core/modules
|
|
//
|
|
include { FASTQC } from '../modules/nf-core/fastqc/main'
|
|
include { FALCO } from '../modules/nf-core/falco/main'
|
|
include { MULTIQC } from '../modules/nf-core/multiqc/main'
|
|
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
|
|
include { CAT_FASTQ as MERGE_RUNS } from '../modules/nf-core/cat/fastq/main'
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
RUN MAIN WORKFLOW
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
// Info required for completion email and summary
|
|
def multiqc_report = []
|
|
|
|
workflow TAXPROFILER {
|
|
|
|
ch_versions = Channel.empty()
|
|
ch_multiqc_logo= Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")
|
|
adapterlist = params.shortread_qc_adapterlist ? file(params.shortread_qc_adapterlist) : []
|
|
|
|
if ( params.shortread_qc_adapterlist ) {
|
|
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}"
|
|
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}"
|
|
}
|
|
|
|
/*
|
|
SUBWORKFLOW: Read in samplesheet, validate and stage input files
|
|
*/
|
|
INPUT_CHECK (
|
|
ch_input
|
|
)
|
|
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
|
|
|
|
// Save final FASTA reads if requested, as otherwise no processing occurs on FASTA
|
|
|
|
|
|
DB_CHECK (
|
|
ch_databases
|
|
)
|
|
ch_versions = ch_versions.mix(DB_CHECK.out.versions)
|
|
|
|
/*
|
|
MODULE: Run FastQC
|
|
*/
|
|
ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
|
|
|
|
if ( params.preprocessing_qc_tool == 'falco' ) {
|
|
FALCO ( ch_input_for_fastqc )
|
|
ch_versions = ch_versions.mix(FALCO.out.versions.first())
|
|
} else {
|
|
FASTQC ( ch_input_for_fastqc )
|
|
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
|
|
}
|
|
/*
|
|
SUBWORKFLOW: PERFORM PREPROCESSING
|
|
*/
|
|
|
|
if ( params.perform_shortread_qc ) {
|
|
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq, adapterlist ).reads
|
|
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
|
|
} else {
|
|
ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
|
|
}
|
|
|
|
if ( params.perform_longread_qc ) {
|
|
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
|
|
.map { it -> [ it[0], [it[1]] ] }
|
|
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
|
|
} else {
|
|
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
|
|
}
|
|
|
|
/*
|
|
SUBWORKFLOW: COMPLEXITY FILTERING
|
|
*/
|
|
|
|
// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
|
|
if ( params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp' ) {
|
|
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
|
|
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
|
|
} else {
|
|
ch_shortreads_filtered = ch_shortreads_preprocessed
|
|
}
|
|
|
|
/*
|
|
SUBWORKFLOW: HOST REMOVAL
|
|
*/
|
|
|
|
if ( params.perform_shortread_hostremoval ) {
|
|
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_shortread_reference_index ).reads
|
|
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
|
|
} else {
|
|
ch_shortreads_hostremoved = ch_shortreads_filtered
|
|
}
|
|
|
|
if ( params.perform_longread_hostremoval ) {
|
|
ch_longreads_hostremoved = LONGREAD_HOSTREMOVAL ( ch_longreads_preprocessed, ch_reference, ch_longread_reference_index ).reads
|
|
ch_versions = ch_versions.mix(LONGREAD_HOSTREMOVAL.out.versions)
|
|
} else {
|
|
ch_longreads_hostremoved = ch_longreads_preprocessed
|
|
}
|
|
|
|
if ( params.perform_runmerging ) {
|
|
|
|
ch_reads_for_cat_branch = ch_shortreads_hostremoved
|
|
.mix( ch_longreads_hostremoved )
|
|
.map {
|
|
meta, reads ->
|
|
def meta_new = meta.clone()
|
|
meta_new.remove('run_accession')
|
|
[ meta_new, reads ]
|
|
}
|
|
.groupTuple()
|
|
.map {
|
|
meta, reads ->
|
|
[ meta, reads.flatten() ]
|
|
}
|
|
.branch {
|
|
meta, reads ->
|
|
// we can't concatenate files if there is not a second run, we branch
|
|
// here to separate them out, and mix back in after for efficiency
|
|
cat: ( meta.single_end && reads.size() > 1 ) || ( !meta.single_end && reads.size() > 2 )
|
|
skip: true
|
|
}
|
|
|
|
ch_reads_runmerged = MERGE_RUNS ( ch_reads_for_cat_branch.cat ).reads
|
|
.mix( ch_reads_for_cat_branch.skip )
|
|
.map {
|
|
meta, reads ->
|
|
[ meta, [ reads ].flatten() ]
|
|
}
|
|
.mix( INPUT_CHECK.out.fasta )
|
|
|
|
ch_versions = ch_versions.mix(MERGE_RUNS.out.versions)
|
|
|
|
} else {
|
|
ch_reads_runmerged = ch_shortreads_hostremoved
|
|
.mix( ch_longreads_hostremoved, INPUT_CHECK.out.fasta )
|
|
}
|
|
|
|
/*
|
|
SUBWORKFLOW: PROFILING
|
|
*/
|
|
|
|
PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
|
|
ch_versions = ch_versions.mix( PROFILING.out.versions )
|
|
|
|
/*
|
|
SUBWORKFLOW: VISUALIZATION_KRONA
|
|
*/
|
|
if ( params.run_krona ) {
|
|
VISUALIZATION_KRONA ( PROFILING.out.classifications, PROFILING.out.profiles, DB_CHECK.out.dbs )
|
|
ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
|
|
}
|
|
|
|
/*
|
|
SUBWORKFLOW: PROFILING STANDARDISATION
|
|
*/
|
|
if ( params.run_profile_standardisation ) {
|
|
STANDARDISATION_PROFILES ( PROFILING.out.classifications, PROFILING.out.profiles, DB_CHECK.out.dbs, PROFILING.out.motus_version )
|
|
ch_versions = ch_versions.mix( STANDARDISATION_PROFILES.out.versions )
|
|
}
|
|
|
|
/*
|
|
MODULE: MultiQC
|
|
*/
|
|
|
|
CUSTOM_DUMPSOFTWAREVERSIONS (
|
|
ch_versions.unique().collectFile(name: 'collated_versions.yml')
|
|
)
|
|
|
|
|
|
workflow_summary = WorkflowTaxprofiler.paramsSummaryMultiqc(workflow, summary_params)
|
|
ch_workflow_summary = Channel.value(workflow_summary)
|
|
|
|
methods_description = WorkflowTaxprofiler.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
|
|
ch_methods_description = Channel.value(methods_description)
|
|
|
|
ch_multiqc_files = Channel.empty()
|
|
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
|
|
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
|
|
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
|
|
|
|
if ( params.preprocessing_qc_tool == 'falco' ) {
|
|
// only mix in files acutally used by MultiQC
|
|
ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt
|
|
.map { meta, reports -> reports }
|
|
.flatten()
|
|
.filter { path -> path.name.endsWith('_data.txt')}
|
|
.ifEmpty([]))
|
|
} else {
|
|
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
|
|
}
|
|
|
|
|
|
if (params.perform_shortread_qc) {
|
|
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
|
}
|
|
|
|
if (params.perform_longread_qc) {
|
|
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
|
}
|
|
|
|
if (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp'){
|
|
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
|
}
|
|
|
|
if (params.perform_shortread_hostremoval) {
|
|
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
|
|
}
|
|
|
|
if (params.perform_longread_hostremoval) {
|
|
ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
|
|
}
|
|
|
|
ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
|
|
|
if ( params.run_profile_standardisation ) {
|
|
ch_multiqc_files = ch_multiqc_files.mix( STANDARDISATION_PROFILES.out.mqc.collect{it[1]}.ifEmpty([]) )
|
|
}
|
|
|
|
MULTIQC (
|
|
ch_multiqc_files.collect(),
|
|
ch_multiqc_config.toList(),
|
|
ch_multiqc_custom_config.toList(),
|
|
ch_multiqc_logo.toList()
|
|
)
|
|
multiqc_report = MULTIQC.out.report.toList()
|
|
}
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
COMPLETION EMAIL AND SUMMARY
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
workflow.onComplete {
|
|
if (params.email || params.email_on_fail) {
|
|
NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
|
|
}
|
|
NfcoreTemplate.summary(workflow, params, log)
|
|
if (params.hook_url) {
|
|
NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
|
|
}
|
|
}
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
THE END
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|