mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-29 08:49:54 +00:00
261 lines
10 KiB
Text
261 lines
10 KiB
Text
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
VALIDATE INPUTS
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
|
|
|
|
// Validate input parameters
|
|
WorkflowTaxprofiler.initialise(params, log)
|
|
|
|
// TODO nf-core: Add all file path parameters for the pipeline to the list below
|
|
// Check input path parameters to see if they exist
|
|
def checkPathParamList = [ params.input, params.databases, params.shortread_hostremoval_reference,
|
|
params.shortread_hostremoval_index, params.multiqc_config
|
|
]
|
|
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
|
|
|
|
// Check mandatory parameters
|
|
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
|
|
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
|
|
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."
|
|
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"
|
|
|
|
if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
|
|
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." }
|
|
|
|
if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
|
|
if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
CONFIG FILES
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
|
|
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
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 { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
|
|
include { PROFILING } from '../subworkflows/local/profiling'
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
IMPORT NF-CORE MODULES/SUBWORKFLOWS
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
//
|
|
// MODULE: Installed directly from nf-core/modules
|
|
//
|
|
include { FASTQC } from '../modules/nf-core/modules/fastqc/main'
|
|
include { MULTIQC } from '../modules/nf-core/modules/multiqc/main'
|
|
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
|
|
|
|
include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main'
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
RUN MAIN WORKFLOW
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
// Info required for completion email and summary
|
|
def multiqc_report = []
|
|
|
|
workflow TAXPROFILER {
|
|
|
|
ch_versions = Channel.empty()
|
|
|
|
/*
|
|
SUBWORKFLOW: Read in samplesheet, validate and stage input files
|
|
*/
|
|
INPUT_CHECK (
|
|
ch_input
|
|
)
|
|
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
|
|
|
|
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 )
|
|
|
|
FASTQC (
|
|
ch_input_for_fastqc
|
|
)
|
|
|
|
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
|
|
|
|
/*
|
|
SUBWORKFLOW: PERFORM PREPROCESSING
|
|
*/
|
|
if ( params.perform_shortread_clipmerge ) {
|
|
|
|
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
|
|
} else {
|
|
ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
|
|
}
|
|
|
|
if ( params.perform_longread_clip ) {
|
|
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.first())
|
|
} else {
|
|
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
|
|
}
|
|
|
|
/*
|
|
SUBWORKFLOW: COMPLEXITY FILTERING
|
|
*/
|
|
|
|
if ( params.perform_shortread_complexityfilter ) {
|
|
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
|
|
} 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_reference_index ).reads
|
|
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
|
|
} else {
|
|
ch_shortreads_hostremoved = ch_shortreads_filtered
|
|
}
|
|
|
|
if ( params.perform_runmerging ) {
|
|
|
|
ch_reads_for_cat_branch = ch_shortreads_hostremoved
|
|
.mix( ch_longreads_preprocessed )
|
|
.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 = CAT_FASTQ ( ch_reads_for_cat_branch.cat ).reads
|
|
.mix( ch_reads_for_cat_branch.skip )
|
|
.map {
|
|
meta, reads ->
|
|
[ meta, [ reads ].flatten() ]
|
|
}
|
|
|
|
} else {
|
|
ch_reads_runmerged = ch_shortreads_hostremoved
|
|
.mix( ch_longreads_preprocessed )
|
|
}
|
|
|
|
/*
|
|
SUBWORKFLOW: PROFILING
|
|
*/
|
|
|
|
PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
|
|
ch_versions = ch_versions.mix( PROFILING.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)
|
|
|
|
ch_multiqc_files = Channel.empty()
|
|
ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
|
|
ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
|
|
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
|
|
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
|
|
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
|
|
|
|
if (params.perform_shortread_clipmerge) {
|
|
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
|
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
|
|
}
|
|
|
|
if (params.perform_longread_clip) {
|
|
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
|
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
|
|
}
|
|
|
|
if (params.perform_shortread_complexityfilter){
|
|
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
|
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
|
|
}
|
|
|
|
if (params.perform_shortread_hostremoval) {
|
|
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
|
|
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
|
|
}
|
|
|
|
if (params.perform_runmerging){
|
|
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
|
|
}
|
|
|
|
ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )
|
|
|
|
// TODO create multiQC module for metaphlan
|
|
MULTIQC (
|
|
ch_multiqc_files.collect()
|
|
)
|
|
multiqc_report = MULTIQC.out.report.toList()
|
|
ch_versions = ch_versions.mix(MULTIQC.out.versions)
|
|
}
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
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)
|
|
}
|
|
|
|
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
THE END
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|