Error in rule rijk_zscore:

[houruiyan]

Hello, thank you for your great tools! I meet some trouble when I use them. Hope to get your help!
I installed successfully this package. But when I tried to run the test data, I met this error.

[juliaolivieri]

there should be a file ending in .err in the folder job_output in the directory. Could you share the error message from that file? We also have a nextflow implementation of the pipeline that may be easier to use on your system: https://github.com/salzmanlab/SpliZ

[houruiyan]

Thank you very much for your quick reply!
I found the rijk_zscore_test_0.1_0.0_5.err in the job_output folder. The content of it is like this:

There are also another .err file in the folder job_output : tsv2pq_test.err. It does not include any content.

Hope to get your reply. Thank you!

[houruiyan]

Thank you. The nextflow implementation of the pipeline works! It is great!

[wook2014]

I meet the same problem RuntimeError: required column 'refName_newR1' is missing when running with test data. It seemed that the test data lacks of refName_newR1 column that lead to this problem. And there is some differences between the SICILIAN output and required columns in names such as "barcode" and "cell".