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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_VARIANT_ANALYSIS_WF } from './workflows/minor_variant_analysis_wf.nf'
include { QUALITY_CHECK_WF } from './workflows/quality_check_wf.nf'
include { REPORTS_WF } from './workflows/reports_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) {
VALIDATE_FASTQS_WF(params.input_samplesheet)
} else if (params.only_pre_merge_analysis) {
validated_reads_ch = VALIDATE_FASTQS_WF( params.input_samplesheet )
QUALITY_CHECK_WF( validated_reads_ch )
MAP_WF( validated_reads_ch )
CALL_WF( MAP_WF.out.sorted_reads_ch )
MINOR_VARIANT_ANALYSIS_WF(CALL_WF.out.reformatted_lofreq_vcfs_tuple_ch)
UTILS_MERGE_COHORT_STATS ( MINOR_VARIANT_ANALYSIS_WF.out.approved_samples_ch,
MINOR_VARIANT_ANALYSIS_WF.out.rejected_samples_ch,
CALL_WF.out.cohort_stats_tsv )
}
//FIXME IMPLEMENT ANOTHER LOGIC FOR --only_merge_analysis
/* else if { */
/* //--cohort_data --only_merge_wf */
/* } */
} else {
//NOTE: If no --only* option specified, run the entire analysis
validated_reads_ch = VALIDATE_FASTQS_WF( params.input_samplesheet )
QUALITY_CHECK_WF( validated_reads_ch )
MAP_WF( validated_reads_ch )
CALL_WF( MAP_WF.out.sorted_reads_ch )
MINOR_VARIANT_ANALYSIS_WF(CALL_WF.out.reformatted_lofreq_vcfs_tuple_ch)
MERGE_WF( CALL_WF.out.gvcf_ch,
CALL_WF.out.reformatted_lofreq_vcfs_tuple_ch,
CALL_WF.out.cohort_stats_tsv,
MINOR_VARIANT_ANALYSIS_WF.out.approved_samples_ch,
MINOR_VARIANT_ANALYSIS_WF.out.rejected_samples_ch)
REPORTS_WF(QUALITY_CHECK_WF.out.reports_fastqc_ch,
MINOR_VARIANT_ANALYSIS_WF.out.minor_variants_results_ch,
MERGE_WF.out.major_variants_results_ch)
}
}
}