nextflow.enable.dsl=2 /* Testing pipeline for marseq scRNASeq analysis */ include { mapping; } from "./nf_modules/bwa/main.nf" include { sort_bam; } from "./nf_modules/samtools/main.nf" include { germline_cohort_data_variant_calling; } from "./nf_modules/gatk4/main.nf" addParams( variant_calling_out: "vcf/", ) params.fastq = "" params.fasta = "" channel .fromFilePairs( params.fastq, size: -1) .set { fastq_files } channel .fromPath( params.fasta ) .map { it -> [it.simpleName, it]} .set { fasta_files } workflow { mapping(fasta_files, fastq_files) sort_bam(mapping.out.bam) germline_cohort_data_variant_calling(sort_bam.out.bam, fasta_files) }