Unexpected concatenation of processes ext {} map in profiles directive

[dwishsan]

Hello,

First of all, I do not know if this is a bug or a feature or a bad usage of Nextflow, but it does looks like a bug to me!

Bug report

I have a file names profiles.config where I define the profiles for my workflow.
I have a test profile where I am configuring all my process so they can work on a minimal input.

Let's say that I have this in my profiles.config:

profiles {
  test {
    process {
      withName:'FOO' {
        ext {
          foo = 'foo'
        }
      }
      withName:'BAR' {
        ext {
          bar = 'bar'
        }
      }
      withName:'DOES_NOT_MATCH_ANYTHING' {
        ext {
          test = 'test'
        }
      }
    }
  }
}

Expected behavior and actual behavior

The expected behavior is that I will only have access to task.ext.foo in the FOO process & task.ext.bar in the BAR process.

The actual behavior is that I have access task.ext.foo, task.ext.bar and task.ext.test in the FOO and BAR process.
It seems that when multiple ext {} are used, they are concatenated and then attributed to each process calling ext {}.

Using ext.<> rather than ext {} or only one ext {} for a process and ext.<> for other processes produce the expected behavior. So, the following works as expected:

profiles {
  test {
    process {
      withName:'FOO' {
        ext.foo = 'foo'
      }
      withName:'BAR' {
       ext.bar = 'bar'
      }
      withName:'DOES_NOT_MATCH_ANYTHING' {
        ext.test = 'test'
      }
    }
  }
}

profiles {
  test {
    process {
      withName:'FOO' {
        ext {
          foo = 'foo'
        }
      }
      withName:'BAR' {
        ext.bar = 'bar'
      }
      withName:'DOES_NOT_MATCH_ANYTHING' {
        ext.test = 'test'
      }
    }
  }
}

Also, using the process {} outside profiles {} produce the expected behavior:

process {
  withName:'FOO' {
    ext {
      foo = 'foo'
    }
  }
  withName:'BAR' {
    ext {
      bar = 'bar'
    }
  }
  withName:'DOES_NOT_MATCH_ANYTHING' {
    ext {
      test = 'test'
    }
  }
}

Environment

• Nextflow version: 23.05.0
• Java version: [?]
• Operating system: Linux
• Bash version: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)

[bentsherman]

I wonder if this issue is fixed by the config parser that we are developing #4744 . Might be worth building that PR and testing to see if the issue goes away

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.