nextflow.enable.dsl=2 /* ./nextflow src/solution_RNASeq_DSL2.nf --fastq "data/tiny_dataset/fastq/tiny2_R{1,2}.fastq.gz" --fasta "data/tiny_dataset/fasta/tiny_v2_10.fasta" --bed "data/tiny_dataset/annot/tiny.bed" -profile docker */ log.info "fastq files : ${params.fastq}" log.info "fasta file : ${params.fasta}" log.info "bed file : ${params.bed}" Channel .fromPath( params.fasta ) .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" } .set { fasta_files } Channel .fromPath( params.bed ) .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" } .set { bed_files } Channel .fromFilePairs( params.fastq ) .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" } .set { fastq_files } include { adaptor_removal_pairedend } from './nf_modules/cutadapt/main' include { trimming_pairedend } from './nf_modules/urqt/main' include { fasta_from_bed } from './nf_modules/bedtools/main' include { index_fasta; mapping_fastq_pairedend } from './nf_modules/kallisto/main' workflow { adaptor_removal_pairedend(fastq_files) trimming_pairedend(adaptor_removal_pairedend.out.fastq) fasta_from_bed(fasta_files, bed_files) index_fasta(fasta_from_bed.out.fasta) mapping_fastq_pairedend(index_fasta.out.index.collect(), trimming_pairedend.out.fastq) }