'run_check' was not defined error

[Concetta De Quattro]

Hi,

I am using JAFFA and I performing a first test with the example data provided by the JAFFA website.
I downloaded JAFFA and installed following the instructions on the website.

Subsequently I ran JAFFA in the assembly mode with the following command:
<full_path>/tools/bin/bpipe run <full_path>/JAFFA_assembly.groovy <full_path>/jaffa_test/*.gz

After that I got this error:

WARN: Error evaluating script /home/stefania/JAFFA-version-1.09/JAFFA_stages.groovy: No such property: stefania for class: JAFFA_stages_bpipe
WARN: Error evaluating script /home/stefania/JAFFA-version-1.09/JAFFA_stages.groovy: No such property: stefania for class: JAFFA_stages_bpipe
====================================================================================================| Starting Pipeline at 2019-07-18 14:16 |====================================================================================================
Pipeline Failed!
A variable referred to in your script on line 20, 'run_check' was not defined.
Please check that all pipeline stages or other variables you have referenced by this name are defined.

I tried to modify the JAFFA_stages.groovy, changing the path of the genome but I still had this error.
It looks like that JAFFA misses some dependencies. How can I fix this error? Should I check anything else?

Thank you!

Concetta

[Nadia Davidson]

Hi,

Did you change some of the variables in the .groovy file before you got this error?

Did you put quotes around any paths you set?

Cheers,

Nadia.