Now we can start to use the flexibility nextflow provides to name our output files dynamically based on sample name and we also can start to scale up by using the wildcard to grab all the fastq files in our example ‘reads’ directory. Here nextflow is going to create a new separate process for each of our samples.

process CUTADAPT { __ __ publishDir __ “results/”, mode: “copy”__ __ input:__ __ path __ reads_var __ output:__ __ path “${__ reads_var.simpleName }_ trimmed.fastq ” __ script:__ __ “”"__ __ __ cutadapt __ -a AACCGGTT -o ${__ reads_var.simpleName }_ trimmed.fastq __ $__ reads_var __ “”"__ } workflow { __ CUTADAPT(__ Channel.fromPath (’*. fastq __’, __ checkIfExists : true)) }