Here’s how we could link the trim, align and variant calling together. So now we’ll put it all together and run the entire workflow from end to end on the system.

workflow {

reads_ch = Channel.fromPath("${params.reads_dir}/*.fastq", checkIfExists:  true)

trimmed_ch = CUTADAPT(reads_ch)

aligned_ch = BWA_ALIGN(trimmed_ch)

FREEBAYES(aligned_ch)

}