Cellranger error from strato --backend flag

[Adam Rubin]

Hello, 

I ran into an error using the latest Cumulus 2.6.3 cellranger where mkfastq failed at the first call of strato with the following error: "strato cp: error: the following arguments are required: --backend" It seems you dealt with a similar error in April: https://groups.google.com/g/cumulus-support/c/TGqz1OZgw3A/m/h_tq_k40AQAJ 

I seemed to have bypassed it by using cellranger_arc version 2.0.2 and reverting to Cumulus 2.6.0. 

Thanks a lot!

Best,

Adam

[Yiming Yang]

Hello Adam,

Sorry for this inconvenience. The issue is because the mkfastq step uses an internal docker image only open to Broad users, and our team no longer has access to update it. Your bypassing approach is probably the only way if you want to use the mkfastq feature in our workflow.

However, since mkfastq is marked as deprecated in Cell Ranger v9.0, and will be removed later, we also will drop this step from our workflow in next release. For generating fastq from BCL folders, you can either use Broad's BCLConvert workflow, or do it locally.

Sincerely,

Yiming

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