Process Guide

Outputs

All the output nodes for a new process are defined in this section. In a process similar to that of adding inputs, you can click the Add output... dropdown menu to select from a list of output parameters. Once an output has been chosen, you'll see an Output Name box, as well as an Add/Remove Operator button (wrench icon) and an Operators button.

You can select output files created by the process by using the Output Name box. Entering a pattern of output files will highlight and grab all files starting with that pattern; for instance, entering "genome.index*" in this field will grab all the files whose names begin with "genome.index." You can also use Nextflow variables, which are defined in the Inputs and Scripts sections. Here are some examples of input and output qualifiers and names:

Input Qualifier	Input name	Output Qualifier	Output name
file	genome	file	"${genome}_out.txt"
set	val(name), file(reads)	set	val(name), file("${name}.unmap*.fq")
set	val(name), file(reads)	file	"${name}.bam"
set	val(name), file(genome)	file	"genome.index*"

Additionally, if you need to transform values emitted by a channel, you can click the Add/Remove Operator button, then select operators from the Operators dropdown menu that appears.

• A Note on Optional Outputs:

If your process doesn't generate some outputs in some circumstances, you can check the Optional checkbox, which tells Nextflow not to fail and exit the process if the given output is not created.