publish-rename-outputs.adoc

Rename process outputs

Problem

You need to store the outputs of a process to a directory giving files a name of your choice.

Solution

The publishDir allows you to store the process outputs in a directory of your choice.

Specify the saveAs parameter to give each file a name of your choice proving a custom rule as a closure.

Code

process foo {
 publishDir 'results', saveAs: { filename -> "foo_$filename" }

 output:
 file '*.txt'

 '''
 touch this.txt
 touch that.txt
 '''
}

Run it

nextflow run patterns/publish-rename-outputs.nf

Save outputs in a sub-directory

The same pattern can be used to store specific files in separate directories depending the actual name.

process foo {
 publishDir 'results', saveAs: { filename -> filename.endsWith(".zip") ? "zips/$filename" : filename }

 output:
 file '*'

 '''
 touch this.txt
 touch that.zip
 '''
}

Tip	Relative paths are resolved against the publishDir store path. Use an absolute path to store files in a directory outside the publishDir store path.

Run it

nextflow run patterns/publish-rename-outputs-subdirs.nf