main.nf

#!/usr/bin/env nextFlow
nextflow.enable.dsl=2
// Import modules
include { GET_ANALYSISES } from "./modules/get_analysises/main.nf"
// Import subworkflows
include { SCRNASEQ } from "./subworkflows/scrnaseq.nf"
include { FLEX_SCRNASEQ } from "./subworkflows/flexscrnaseq.nf"
include { SCCITESEQ } from "./subworkflows/scciteseq.nf"
include { SC_ATAC } from "./subworkflows/scatac.nf"
include { SC_ARC } from "./subworkflows/scarc.nf"
include { SCMULTI } from "./subworkflows/scmulti.nf"
include { VISIUM } from "./subworkflows/visium.nf"

workflow {
	samplesheet_ch = GET_ANALYSISES(params.samplesheet)
	pipeline_ch = samplesheet_ch
        .splitCsv(header:true)
        .map { row -> tuple( row.pipeline ) }
		.unique()
		.collect()
	
	if (pipeline_ch.contains('scrna-10x')) {
		rna_workflow = SCRNASEQ()
	} 
	if (pipeline_ch.contains('scflex-10x')) {
		flex_worfklow = FLEX_SCRNASEQ()
	}
	if (pipeline_ch.contains('scciteseq-10x')) {
		SCCITESEQ()
	}
	if (pipeline_ch.contains('scatac-10x')) {
		SC_ATAC()
	} 
	if (pipeline_ch.contains('scarc-10x')) {
		SC_ARC()
	}
	if (pipeline_ch.contains('scmulti-10x')) {
		SCMULTI()
	}
	if (pipeline_ch.contains('scvisium-10x')) {
		VISIUM()
	}
}