Error running Sequential mode with external assemblies

[r-frizzo]

Hello! I have found an issue when running the pipeline in sequential mode with external assemblies.

I've fixed issue #743 as you suggested, but then ran into another problem:

The external assembly path provided in the "samples" file is recognized, prompting the message: "External assembly provided: . Overriding assembly" then the path information is somehow lost, resulting in the message: "Can't find assembly file"

I think the error is around the if statement at line 71 of 01.run_all_assemblies.pl. I've changed line 72 from

$outassembly=$extassembly; 

to

$extassembly=$extassemblies{$asamples}; $outassembly=$extassembly;

and managed to get the pipeline going.

Would this work or would you suggest a better fix?

Thank you and have a nice evening, Riccardo

sequential_extassembly.zip

[jtamames]

Hello! I myself ran into this bug last week, and corrected it just as you did. Thank you for this! Best, J

[r-frizzo]

Awesome! Thank you!