main.nf - No such variable: var_ch1 - Githubissues

SBIMB / StellarPGx

Calling star alleles in highly polymorphic pharmacogenes (e.g. CYP450 genes) by leveraging genome graph-based variant detection.

MIT License

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main.nf - No such variable: var_ch1 #13

Closed TonyLupara closed 2 years ago

TonyLupara commented 2 years ago

When I try "dry run" command: nextflow run main.nf -profile standard,test

I get error message:

No such variable: var_ch1 -- Check script 'main.nf' at line: 501 or see '.nextflow.log' file for more details

twesigomwedavid commented 2 years ago

@TonyLupara,

Thanks. May you provide some details of the machine you're using to do the test run. It appears your installation of StellarPGx may have been incomplete. To provide you with better assistance on this, kindly refer to the bug report template here (https://github.com/SBIMB/StellarPGx/issues/new?assignees=&labels=&template=bug_report.md&title=)

The channel var_ch1 is created at line 354, https://github.com/SBIMB/StellarPGx/blob/a6962a72f18550c06d4c7eaa07b1ad2c91eaa7c8/main.nf#L354. Therefore, it's strange that your error message says it's missing when it comes to line 501.