Running the pipeline in targeted mode without specifying --panel gives the following error message:
ERROR ~
The null is not defined. Currently, the available panels are:
- tso500
Looking at the code, the first if block was not triggered when it should have done, and so the second was used:
if (!params.containsKey('panel')) {
def panels = Constants.PANELS_DEFINED.join('\n - ')
log.error "\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" A panel is required to be set using the --panel CLI argument or in a \n" +
" configuration file.\n" +
" Currently, the available panels are:\n" +
" - ${panels}\n" +
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
Nextflow.exit(1)
} else if (!Constants.PANELS_DEFINED.contains(params.panel)) {
def panels = Constants.PANELS_DEFINED.join('\n - ')
log.error "\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" The ${params.panel} is not defined. Currently, the available panels are:\n" +
" - ${panels}\n" +
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
Nextflow.exit(1)
}
Running the pipeline in targeted mode without specifying
--panel
gives the following error message:ERROR ~
Looking at the code, the first
if
block was not triggered when it should have done, and so the second was used: