Closed sweavs111 closed 3 months ago
I get the same error with --grna_integration_strategy singleton
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Thank you both for identifying this bug. I will take a look in the near future and get back to you!
Hi Seth,
Thank you for your detailed report. I think I fixed the problem. Could you download and install the latest version of the sceptre
package and try again?
Hey Tim,
I ran the trial pipeline with both bonferroni and singleton integration methods and it completed. Thanks for the quick fix!
Great Seth, let us know if you encounter any other issues with the pipeline.
Hello,
I am running the nextflow pipeline, and it is failing at the run_qc step when I use the bonferroni gRNA integration strategy. The pipeline runs just fine for me if I remove the
--grna_integration_strategy bonferroni
argument from the nextflow script (therefore using "union") and completes. Same exact input files used. Is this a known issue? Is there anything I can do to fix it?I tracked down the bug to the run_qc.R file line 43:
sceptre_object <- do.call(what = sceptre::run_qc, args = args_to_pass)
I tried to look into it further but got stuck.
See screenshot and nextflow error message:
Let me know if you would like me to send over any of my .rds or .odm files for replicating the error. Thanks!