A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Dear all,
is it possible to write plain java/groovy in the *setup* section instead of a nf code ? Something like:

```setup {
script:
"""
Files.writeString(Paths.get("test1.bed"), "chr1\t10\t100\n");
"""
}```
Thank you

so I'd say that you should be able to do something along these lines

<@U03DZ1KA8F2> might have more insight than me on that, given his initial code in <#CP3RJSMF0|> was my inspiration for what I put in <#CGFUX04HZ|> :

<https://github.com/nf-core/sarek/blob/dev/tests/lib/UTILS.groovy>
<https://github.com/nf-core/sarek/blob/dev/tests/aligner-bwa-mem.nf.test>

no script needed in the setup block and also groovy outside setup is also cool :party-groovy:

Yes it's pretty flexible :slightly_smiling_face: I don't remember who anymore but someone made setup blocks entirely using groovy code

Yes, you can write whatever arbitrary Groovy you want. I use it to stage database files prior to the test:

<https://github.com/sanger-tol/metagenomeassembly/blob/main/tests/default.nf.test>

One suggestion - if you're writing any files for the test, you can use the variable `$launchDir` which points to the directory `.nf-test/tests/&lt;hash&gt;/` , which makes sure that the files stay contained to the specific test and makes cleanup nice and easy.

Note also the undocumented `cleanup {}` block that runs after the test that you can use to clean up anything you did that you don't want to persist!