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

nf-core

Just wanted to re-highlight that some cleanup between tests would be really helpful: <https://github.com/askimed/nf-test/issues/315#issuecomment-4198293554>

I don't know how much this would break things, but you could just delete the launchDir in the `cleanup` block for now. Perhaps you could gate it behind an env var that's set on the GH runner so it doesn't run during local testing.

```
    test("-profile test") {

        setup {
            ...
        }

        when {
            ...
        }

        then {
            ...
        }

        cleanup {
            new File("${launchDir}").deleteDir()
        }

    }
}```

Don't think it would help with docker images though

I wonder if:

```                                                                                                                                                                                                                                                                             
  cleanup {                                                                                                                                                                                                                                                                  
      "docker system prune -f".execute()                                                                                                                                                                                                                                     
      new File("${launchDir}").deleteDir()                                                                                                                                                                                                                                   
  }      ```
... would work

You can run arbitrary subprocesses from Groovy too...  an example I use:

```            def checkm2_db_url  = "<https://tolit.cog.sanger.ac.uk/test-data/resources/metagenomeassembly/checkm2_database.tar.gz>"
            def checkm2_command = ['bash', '-c', "curl -L --retry 5 ${checkm2_db_url} | tar xzf - -C ${launchDir}"]
            def checkm2_proc = checkm2_command.execute()
            checkm2_proc.waitFor()```
If there's a Docker command you could run to prune images you could execute that in the cleanup?

I agree and it's one of the features high on my priority list when I'm back to developing nf-test :slightly_smiling_face:

FWIW Jim's solution does work though :slightly_smiling_face:

Good to know! I'll probably take some inspiration from it

Would be nice to be able to access nf-test success outputs in the `cleanup` block - e.g. to only execute if the task succeeded

Just realised I bumped shards at the same time, have bumped back, will let you know if things still pass due to cleanup

&gt; Have you already made an issue for that?
No :smiling_face_with_tear:

<https://github.com/askimed/nf-test/issues/359>

&gt; Just realised I bumped shards at the same time, have bumped back, will let you know if things still pass due to cleanup
Still good

Just cross-linking <https://github.com/nf-core/rnaseq/pull/1816#discussion_r3136226075>