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133 lines
5.0 KiB
Plaintext
133 lines
5.0 KiB
Plaintext
/*
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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.multiqc_config, params.fasta ]
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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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/*
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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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/*
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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 { 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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/*
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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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//
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// MODULE: Run FastQC
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//
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FASTQC (
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INPUT_CHECK.out.reads
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)
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ch_versions = ch_versions.mix(FASTQC.out.versions.first())
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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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//
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// MODULE: MultiQC
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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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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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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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