Nextflow doesn't match the container from the withName section at the nextflow.config file (NFX_VERSION >= 22.03.0-edge).

[CarlosLopezElorduy]

Bug report

When using containers specified in the nextflow.config file (withName section), Nextflow doesn't match them properly in versions >= 22.03.0-edge.

Expected behavior and actual behavior

• EXPECTED: the container from the withName section should be matched properly in any version of Nextflow
• ACTUAL: the container is only matched properly up until version 22.03.0-edge.

Steps to reproduce the problem

Minimum setup to reproduce it:

$ mkdir nfconfig
$ cd nfconfig
$ cat > nextflow.config <<EOF
process {
  withName:Foo {
    container = 'ubuntu'
  }
}
 
profiles {
  bar {
    process {
      withName:Foo {
        cpus = 14
        memory = 60.GB
      }
    }
  }
}
EOF

Program output

The container is matched at the nextflow.config file when using any NXF_VERSION < 22.03.0-edge (e.g. NXF_VERSION = 22.02.1-edge).

$ NXF_VER=22.02.1-edge nextflow config -profile bar
process {
   withName:Foo {
      container = 'ubuntu'
      cpus = 14
      memory = '60 GB'
   }
}

The container is NOT matched when using NXF_VERSION >= 22.03.0-edge.

$ NXF_VER=22.03.0-edge nextflow config -profile bar
process {
   withName:Foo {
      cpus = 14
      memory = '60 GB'
   }
}

Environment

• Nextflow version (WORKING): NXF_VERSION < 22.03.0-edge
• Nextflow version (NOT WORKING): NXF_VERSION >= 22.03.0-edge
• Java version: openjdk 11.0.13 2021-10-19
• Operating system: Linux
• Bash version: 4.2.46(2)-release

Additional context

Maybe related with the fix to this issue https://github.com/nextflow-io/nextflow/issues/2701 found in the release notes for version 22.03.0-edge ?

[jorgeaguileraseqera]

yes, it's a known bug

as a temporary workaround, you can try to declare the profile section firstly:

profiles {
  bar {
    process {
      withName:Foo {
        cpus = 14
        memory = 60.GB
      }
    }
  }
}

process {
  withName:Foo {
    container = 'ubuntu'
  }
}

NXF_VER=22.03.0-edge nextflow config -profile bar
process {                            
   withName:Foo {
      cpus = 14
      memory = '60 GB'
      container = 'ubuntu'
   }
}

[stale[bot]]

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