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ubuntu-shellinabox.yaml

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  • solution_RNASeq.nf 1.29 KiB
    nextflow.enable.dsl=2
    
    /*
    ./nextflow src/solution_RNASeq.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)
    }