Nextflow: Add name to manifest and reject other attributes

[ewels]

It would be great if name (workflow name) and author could be added as valid variables in the manifest scope.

Additionally, if non-standard variable names in the scope could trigger an error that would be helpful.

Thanks!

Phil

[pditommaso]

The author should be already there!

[ewels]

You’re right! My apologies.

[sven1103]

Additionally, if non-standard variable names in the scope could trigger an error that would be helpful.

Hm, if I add a variable that is not part of the controlled vocabulary of the manifest, Nextflow already throws an error. I.e. when I add age = '27' to the manifest scope, and try to access it in the main.nf with workflow.manifest.age, I get:

ERROR ~ No such variable: age

@ewels could you explain me, what you meant? Maybe I did not get the issue properly.

Sven

[ewels]

True, trying to access it throws an error. I more meant to throw an error if you try to just define it.

[pditommaso]

A warning message would be even better.

On Sun, Sep 30, 2018, 14:17 Phil Ewels [e-mail] wrote:

True, trying to access it throws an error. I more meant to throw an error
if you try to just define it.

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[sven1103]

My current code would produce something like this: (dont know, why the warning messages are repeated though)

WARN: 'age' is not a valid manifest field!
WARN: 'pipelineVersion' is not a valid manifest field!
Launching `../hlatyping-workflow/main.nf` [elated_allen] - revision: 61c759c958
WARN: 'age' is not a valid manifest field!
WARN: 'pipelineVersion' is not a valid manifest field!
WARN: The config file defines settings for an unknown process: fastqc
WARN: 'age' is not a valid manifest field!
WARN: 'pipelineVersion' is not a valid manifest field!
WARN: Access to undefined parameter `reads` -- Initialise it to a default value eg. `params.reads = some_value`
=========================================
WARN: Access to undefined parameter `version` -- Initialise it to a default value eg. `params.version = some_value`
 nf-core/hlatyping vnull
=========================================
ERROR ~ No such variable: age

 -- Check script 'main.nf' at line: 109 or see '.nextflow.log' file for more details

[pditommaso]

Is the warning for the same field showed multiple times?

[sven1103]

yes, and i dont know why honestly

[pditommaso]

A patch is available in the latest snapshot 0.32.1-SNAPSHOT.

[pditommaso]

Released with version 18.10.1.