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Document params-file and improve self-update #2673

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Apr 23, 2022
Merged

Document params-file and improve self-update #2673

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Document params-file and improve self-update [ci skip]
abhi18av Feb 24, 2022
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Update docs/cli.rst [ci skip]
abhi18av Feb 24, 2022
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Update docs/cli.rst [ci skip]
abhi18av Feb 24, 2022
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pditommaso Apr 23, 2022
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9 changes: 8 additions & 1 deletion docs/cli.rst
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Expand Up @@ -1265,6 +1265,12 @@ facilitates rapid iterations, inspections of any pipeline as well as debugging.
$ nextflow run nextflow-io/hello -with-tower


- Invoke the nextflow pipeline execution with a custom parameters ``YML`` file.
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The parameters which are specified through this mechanism are merged with the resolved configuration (base configuration and profiles) and only the common fields are overwritten by the ``YML`` file.::
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The params file can be YAML or JSON. I would say YAML/JSON file instead of YML file.

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Also @pditommaso we should clarify what happens if you provide params through a config file and a params file via CLI arguments. I think the params file takes priority but I'm not certain.

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Yes, this question has come up recently #2662

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Was missing this conversation. The CLI params overrides the ones the json/yaml file.

You can see it here, it reads the params file and put it into the result map. then if there are cli params copy them over the result map.

nextflow/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

Lines 496 to 513 in 0f63f1a

final result = [:]
final file = getParamsFile()
if( file ) {
def path = validateParamsFile(file)
def type = path.extension.toLowerCase() ?: null
if( type == 'json' )
readJsonFile(path, configVars, result)
else if( type == 'yml' || type == 'yaml' )
readYamlFile(path, configVars, result)
}
// set the CLI params
if( !params )
return result
for( Map.Entry<String,String> entry : params ) {
addParam( result, entry.key, entry.value )
}

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$ nextflow run main.nf -params-file pipeline_params.yml


--------------------
self-update
--------------------
Expand All @@ -1284,7 +1290,8 @@ Update the nextflow runtime to the latest available version.

**Description**

The ``self-update`` command directs the ``nextflow`` cli to update itself to the latest stable release.
The ``self-update`` command directs the ``nextflow`` cli to update itself to the latest stable release.
The ``self-update`` command also updates the `Nextflow launcher script <https://github.com/nextflow-io/nextflow/blob/master/nextflow>`_ in addition to the Java artifacts, whereas the ``NXF_VER`` environment variables only updates the Java artifacts.
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**Examples**
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