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Output of 'config' broken when interpolating into a list #801

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TheRealPJC opened this issue Jul 16, 2018 · 1 comment
Closed

Output of 'config' broken when interpolating into a list #801

TheRealPJC opened this issue Jul 16, 2018 · 1 comment

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@TheRealPJC
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The output of the 'config' command is broken when a parameter uses string interpolation in a list of elements.

For example, running the following command:

nextflow -C my_config.cnf config

on the file 'my_config.cnf' with the following content:

CONST = "SOMETHING"
params {
  interpolated_list = ["${CONST}/a", "b", "c"]
}

should give this i.e. the config as it is after the interpolation of $CONST into the first element in the list:

CONST = 'SOMETHING'
params {
   interpolated_list = ['SOMETHING/a', 'b', 'c']
}

However, the actual output is this:

CONST = 'SOMETHING'
params {
   interpolated_list = [SOMETHING/a, 'b', 'c']
}

The difference is that the first item in the list ("SOMETHING/a") has lost its quotation marks, is not treated as a string, and the output is not a valid Nextflow configuration.

Occurs on Linux and Mac with Nextflow 0.30.1.4844

@pditommaso pditommaso added this to the v19.1.0 milestone Dec 2, 2018
pditommaso added a commit that referenced this issue Dec 2, 2018
This commit fixed an issue when rendering list and map object
defined in the config file containing interpolated string values.
@pditommaso
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Included in version 18.12.0-edge.

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