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main.nf
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main.nf
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nextflow.enable.dsl = 2
//================================================================================
// Include sub-workflows/modules and (soft) override workflow-level parameters
//================================================================================
include { CALL_WF } from './workflows/call_wf.nf'
include { VALIDATE_FASTQS_WF } from './workflows/validate_fastqs_wf.nf'
include { MAP_WF } from './workflows/map_wf.nf'
include { MERGE_WF } from './workflows/merge_wf.nf'
include { MINOR_VARIANTS_ANALYSIS_WF } from './workflows/minor_variants_analysis_wf.nf'
//include { MULTIQC AS MULTIQC_FASTQS } from '../modules/multiqc/multiqc.nf' addParams (params.MULTIQC_FASTQS)
include { QUALITY_CHECK_WF } from './workflows/quality_check_wf.nf'
include { REPORTS_WF } from './workflows/reports_wf.nf'
include { SAMPLESHEET_VALIDATION } from './modules/utils/samplesheet_validation.nf' addParams ( params.SAMPLESHEET_VALIDATION )
include { STRUCTURAL_VARIANTS_ANALYSIS_WF } from './workflows/structural_variants_analysis_wf.nf'
include { UTILS_MERGE_COHORT_STATS } from "./modules/utils/merge_cohort_stats.nf" addParams ( params.UTILS_MERGE_COHORT_STATS )
//================================================================================
// Main workflow
//================================================================================
workflow {
if (params.only_validate_fastqs) {
SAMPLESHEET_VALIDATION( params.input_samplesheet )
VALIDATE_FASTQS_WF( SAMPLESHEET_VALIDATION.out.validated_samplesheet , SAMPLESHEET_VALIDATION.out.status )
QUALITY_CHECK_WF( VALIDATE_FASTQS_WF.out.approved_fastqs_ch )
//TODO: Add modules for generating fastq stats and then capturing them in the MultiQC image
//MULTIQC_FASTQS( QUALITY_CHECK_WF.out.reports_fastqc_ch )
} else {
SAMPLESHEET_VALIDATION(params.input_samplesheet)
validated_reads_ch = VALIDATE_FASTQS_WF( params.input_samplesheet , SAMPLESHEET_VALIDATION.out.status )
QUALITY_CHECK_WF( validated_reads_ch )
MAP_WF( validated_reads_ch )
CALL_WF( MAP_WF.out.sorted_reads_ch )
//NOTE: Samples implicitly get filtered in BCFTOOLS_MERGE if they don't have any identified variants
MINOR_VARIANTS_ANALYSIS_WF(CALL_WF.out.reformatted_lofreq_vcfs_tuple_ch)
UTILS_MERGE_COHORT_STATS( MINOR_VARIANTS_ANALYSIS_WF.out.approved_samples_ch,
MINOR_VARIANTS_ANALYSIS_WF.out.rejected_samples_ch,
CALL_WF.out.cohort_stats_tsv )
all_samples_ch = UTILS_MERGE_COHORT_STATS.out.merged_cohort_stats_ch
.splitCsv(header: false, skip: 1, sep: '\t' )
.map { row -> [
row.first(), // SAMPLE
row.last().toInteger() // ALL_THRESHOLDS_MET
]
}
.map { [ it[0] ] }
//.dump(tag:'MERGE_WF: all_samples_ch', pretty: true)
STRUCTURAL_VARIANTS_ANALYSIS_WF ( validated_reads_ch, all_samples_ch )
if (!params.skip_merge_analysis) {
approved_samples_ch = UTILS_MERGE_COHORT_STATS.out.merged_cohort_stats_ch
.splitCsv(header: false, skip: 1, sep: '\t' )
.map { row -> [
row.first(), // SAMPLE
row.last().toInteger() // ALL_THRESHOLDS_MET
]
}
.filter { it[1] == 1} // Filter out samples which meet all the thresholds
.map { [ it[0] ] }
//.dump(tag:'MERGE_WF: approved_samples_ch', pretty: true)
MERGE_WF( CALL_WF.out.gvcf_ch,
CALL_WF.out.reformatted_lofreq_vcfs_tuple_ch,
approved_samples_ch )
REPORTS_WF( QUALITY_CHECK_WF.out.reports_fastqc_ch,
UTILS_MERGE_COHORT_STATS.out.merged_cohort_stats_ch,
MERGE_WF.out.major_variants_results_ch,
MINOR_VARIANTS_ANALYSIS_WF.out.minor_variants_results_ch,
STRUCTURAL_VARIANTS_ANALYSIS_WF.out.structural_variants_results_ch )
}
}
}