Can't access Cellranger 8.0.0

[David Lieb]

Hi team,

I tried running Cellranger mkfastq with the Cumulus Cellranger workflow on Terra using the default value of cellranger_version and I get the following error:

Task cellranger_mkfastq.run_cellranger_mkfastq:NA:1 failed. The job was stopped before the command finished. PAPI error code 9. Execution failed: generic::failed_precondition: pulling image: docker pull: running ["docker" "pull" "gcr.io/broad-cumulus/cellranger:8.0.0"]: exit status 1 (standard error: "Error response from daemon: manifest for gcr.io/broad-cumulus/cellranger:8.0.0 not found: manifest unknown: Failed to fetch \"8.0.0\" from request \"/v2/broad-cumulus/cellranger/manifests/8.0.0\".\n")

This happens with v 2.6.0 as well as master. If I set  cellranger_version to 7.2.0, it works fine. This is ok for mkfastq, but I will next want to run count and take advantage of any updates in the lastest verison of Cellranger.

Thanks,

David

[Yiming Yang]

Hi David,

Thanks for your interest on using Cumulus workflows.

We've stopped pushing Cellranger and Spaceranger docker images to Broad GCR registry because Broad users now tend to use bcl-convert workflow to generate FASTQ files from BCL. I would suggest you reaching out to Deeptha Srirangam (dsri...@broadinstitute.org) for how to use it.

After achieving FASTQ files, you can then use Cumulus Cellranger workflow by setting "run_mkfastq" input to false, so that the workflow only runs the count step.

Hope it helps.

Sincerely,

Yiming

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γνῶθι σεαυτόν.

[David Lieb]

Hi Yiming,

Thanks for your quick response. I tried the workflow for count with the default Cellranger version and indeed it used version 8.0.0 without a problem.

Best,

David