file and overwrite parameters are ignored

ryandamen commented 10 months ago

Hello,

I tried to use this in one of my pipelines and ran into some issues during testing the example snippets in the README:

plugins {
  id 'nf-prov'
}

prov {
  enabled = true
  formats {
    legacy {
      file = 'manifest.json'
      overwrite = true
    }
  }
}

The first run was successful but while rerunning the same command the overwrite parameter appears to be ignored and returned:

$ nextflow run main.nf -profile dev -stub 
N E X T F L O W  ~  version 23.10.0
Launching `main.nf` [ecstatic_chandrasekhar] DSL2 - revision: 0af3c1836a
Provenance manifest already exists: /mnt/WORKSPACE/xxxx_workspace/projects/test_pipeline/manifest.json

Editing file='manifest.json' to file='test/manifest.json' resulted in the same error. Deleting the manifest and rerunning like this also didn't put the manifest.json within the test folder. This leads me to believe that the file parameter is also ignored.

Did I make a mistake somewhere or do you see something similair?

Kind regards, Ryan

bentsherman commented 10 months ago

Hello Ryan, thanks for pointing it out. I updated the README without noting that this setting would be available in 1.2.0, which I hadn't released yet. I was going to wait for some other in-progress features before releasing, but since that might take a while, I went ahead and cut a new release.

Please try again with the latest plugin version 1.2.0 and let me know if it doesn't work.

ryandamen commented 9 months ago

I tested it out and it works as expected now, Thanks!

nextflow-io / nf-prov

file and overwrite parameters are ignored #20