cellranger_workflow seeming to be incompatible with Cellranger 8.0.0+?

[Laura Drepanos]

Hello,

I ran cellranger_workflow with DataType="rna" and Chemistry="SC3Pv4" and the default cellranger version, and I received an error that SC3Pv4 is not an option, suggesting instead the list of options from prior iterations of cellranger. I then specified cellranger_workflow to use Cellranger 8.0.0 and received the error that the --create-bam argument was not specified, even when explicitly setting the no_bam argument as workflow input. The WDL does not seem to supply the --create-bam in the call to cell ranger, so I was wondering if it is even possible to get transcript counts through this workflow with the use of SC3Pv4, or if I am missing something. 

Thanks!

Laura Drepanos 

[Yiming Yang]

Hello Laura,

May I know which workflow version you are using? From your issue with "--create-bam" option, I highly suspect that you used an old version of our workflow, as this option is only added after Cell Ranger v8.0.0.

Workflow v2.6.3 should work properly with SC3Pv4 chemistry, as it uses Cell Ranger v8.0.1 by default. Actually you can even provide "auto" in Chemistry column and let Cell Ranger figure it out automatically.

We just released v3.0.0 today, which by default runs Cell Ranger v9.0.1. Should also be able to handle the 3' GEM-X chemistry as well.

Sincerely,

Yiming

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