Cumulus Support

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11/26/24

Cellranger error from strato --backend flag

Hello, I ran into an error using the latest Cumulus 2.6.3 cellranger where mkfastq failed at the

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Cellranger error from strato --backend flag

Hello, I ran into an error using the latest Cumulus 2.6.3 cellranger where mkfastq failed at the

11/26/24

Julien Dilly, … Yiming Yang5

9/10/24

Terra CellRanger | Docker access permission denied

Just include Deeptha from Broad into this email thread. Hi Deeptha, As you can read from the quoted

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Terra CellRanger | Docker access permission denied

Just include Deeptha from Broad into this email thread. Hi Deeptha, As you can read from the quoted

9/10/24

8/2/24

Cumulus 2.6.3 is released

Hello All, Cumulus version 2.6.3 is released. This is a small bug-fix release. The release notes can

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Cumulus 2.6.3 is released

Hello All, Cumulus version 2.6.3 is released. This is a small bug-fix release. The release notes can

8/2/24

Francesco Corrado, Yiming Yang3

7/4/24

Workflow error- Cellranger count

Hi Yiming thank you so much for your support!! Now it is working, I will let you know if I have other

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Workflow error- Cellranger count

Hi Yiming thank you so much for your support!! Now it is working, I will let you know if I have other

7/4/24

Andrew Navia, Yiming Yang2

6/28/24

Multiplexed FRP on cellranger_multi

Hi Andrew, It looks like this GitHub issue is yours: https://github.com/lilab-bcb/cumulus/issues/406.

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Multiplexed FRP on cellranger_multi

Hi Andrew, It looks like this GitHub issue is yours: https://github.com/lilab-bcb/cumulus/issues/406.

6/28/24

6/19/24

Cumulus 2.6.2 is released

Hello All, Cumulus version 2.6.2 is released. The release notes can be viewed at https://github.com/

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Cumulus 2.6.2 is released

Hello All, Cumulus version 2.6.2 is released. The release notes can be viewed at https://github.com/

6/19/24

6/12/24

Pegasus 1.10.0 is released

Hello All, Pegasus version 1.10.0 is released, along with PegasusIO version 0.9.1. The new features

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Pegasus 1.10.0 is released

Hello All, Pegasus version 1.10.0 is released, along with PegasusIO version 0.9.1. The new features

6/12/24

5/8/24

Cumulus 2.6.1 is released

Hello All, Cumulus version 2.6.1 is released. The release notes can be viewed at https://github.com/

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Cumulus 2.6.1 is released

Hello All, Cumulus version 2.6.1 is released. The release notes can be viewed at https://github.com/

5/8/24

David Lieb, Yiming Yang3

5/3/24

Can't access Cellranger 8.0.0

Hi Yiming, Thanks for your quick response. I tried the workflow for count with the default Cellranger

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Can't access Cellranger 8.0.0

Hi Yiming, Thanks for your quick response. I tried the workflow for count with the default Cellranger

5/3/24

4/22/24

Cumulus 2.6.0 is released

Hello All, Cumulus version 2.6.0 is released. The release notes can be viewed at https://github.com/

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Cumulus 2.6.0 is released

Hello All, Cumulus version 2.6.0 is released. The release notes can be viewed at https://github.com/

4/22/24

Yuan Lian, Yiming Yang4

4/10/24

Re: workflow error

Thank you for your help Yiming! It works now. Best, Ansel On Tue, Apr 9, 2024 at 5:26 PM Yiming Yang

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Re: workflow error

Thank you for your help Yiming! It works now. Best, Ansel On Tue, Apr 9, 2024 at 5:26 PM Yiming Yang

4/10/24

2/27/24

STARSolo Error: Parsing problem

Hello, I am running into issues when trying to use STARsolo imported to Terra via Dockstore. It seems

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STARSolo Error: Parsing problem

Hello, I am running into issues when trying to use STARsolo imported to Terra via Dockstore. It seems

2/27/24

Laura Domenech, Yiming Yang4

2/26/24

Demultiplexing 2.5 errors

Hello, Just a Demuxlet update: still running with one pool of 2 samples (running time 22h), and still

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Demultiplexing 2.5 errors

Hello, Just a Demuxlet update: still running with one pool of 2 samples (running time 22h), and still

2/26/24

2/3/24

Cumulus 2.5.0 is released

Hello All, Cumulus version 2.5.0 is released. The release notes can be viewed at https://github.com/

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Cumulus 2.5.0 is released

Hello All, Cumulus version 2.5.0 is released. The release notes can be viewed at https://github.com/

2/3/24

David Lieb, Yiming Yang2

1/20/24

Error running Smart-Seq2 workflow on Terra

Hi David, Hope this email finds you well. The issue on missing stratocumulus package has been fixed

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Error running Smart-Seq2 workflow on Terra

Hi David, Hope this email finds you well. The issue on missing stratocumulus package has been fixed

1/20/24

1/20/24

Pegasus 1.9.0 is released

Hello All, Pegasus version 1.9.0 is released, along with PegasusIO version 0.9.0. The new features

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Pegasus 1.9.0 is released

Hello All, Pegasus version 1.9.0 is released, along with PegasusIO version 0.9.0. The new features

1/20/24

Hanna Schumacher

10/18/23

Difference to AnnData?

Hello all, I just discovered Pegasus and am now wondering, what the difference to an AnnData object

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Difference to AnnData?

Hello all, I just discovered Pegasus and am now wondering, what the difference to an AnnData object

10/18/23

Christopher Dall

10/17/23

Trouble with cumulus cellranger count on terra

Hi all, Very new to terra and cellranger, so I will try to provide as much information as possible. I

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Trouble with cumulus cellranger count on terra

Hi all, Very new to terra and cellranger, so I will try to provide as much information as possible. I

10/17/23

Alyssa DuBois, Yiming Yang2

10/12/23

Cumulus ADT adding spaces to file names

Hello Alyssa, Thanks for reaching! May I know the version of Cumulus cellranger workflow that you

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Cumulus ADT adding spaces to file names

Hello Alyssa, Thanks for reaching! May I know the version of Cumulus cellranger workflow that you

10/12/23

dina...@student.ubc.ca, Yiming Yang6

8/25/23

Pegasus human_lung Marker set Issue Inquiry

Dear Dina, Glad it works finally. And thank you very much for reporting these issues to help us

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Pegasus human_lung Marker set Issue Inquiry

Dear Dina, Glad it works finally. And thank you very much for reporting these issues to help us

8/25/23

Rodrigo Martinez Maza, Yiming Yang2

6/26/23

cell ranger_count workflow error

Hello Rodrigo, Can you send me the "generate_count_config.log" file in the execution folder

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cell ranger_count workflow error

Hello Rodrigo, Can you send me the "generate_count_config.log" file in the execution folder

6/26/23

He, Yiwen, Bo Li2

5/28/23

Pegasus installation issues for macOS

Hi Yiming, Can you take a look when you have time? Thanks, Bo Bo Li, Ph.D. Principal Scientist,

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Pegasus installation issues for macOS

Hi Yiming, Can you take a look when you have time? Thanks, Bo Bo Li, Ph.D. Principal Scientist,

5/28/23

4/18/23

Re: help with setting cirrocumulus

Hi Sisi, The localhost approach is used for self-viewing the data interactively without downloading.

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Re: help with setting cirrocumulus

Hi Sisi, The localhost approach is used for self-viewing the data interactively without downloading.

4/18/23

3/22/23

Cumulus on Terra

Hello, I am new to using the Cumulus workflow on Terra and just getting familiar. I am looking to see

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Cumulus on Terra

Hello, I am new to using the Cumulus workflow on Terra and just getting familiar. I am looking to see

3/22/23

Monika Looney, Yiming Yang6

3/14/23

bcl2fastq docker image

Please see my inline comments below. On Mon, Mar 13, 2023 at 11:56 PM Monika Looney <monika.looney

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bcl2fastq docker image

Please see my inline comments below. On Mon, Mar 13, 2023 at 11:56 PM Monika Looney <monika.looney

3/14/23

1/29/23

Cumulus 2.4.0 is released

Hello All, Cumulus version 2.4.0 is released. The release notes can be viewed at https://github.com/

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Cumulus 2.4.0 is released

Hello All, Cumulus version 2.4.0 is released. The release notes can be viewed at https://github.com/

1/29/23

12/16/22

Local PC testing of cumulus / strato pipelines

Hi - I'm working up some pipelines utilising cumulus tooling, including strato. It would be

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Local PC testing of cumulus / strato pipelines

Hi - I'm working up some pipelines utilising cumulus tooling, including strato. It would be

12/16/22

10/31/22

Cumulus 2.3.0 is released

Hello All, Cumulus version 2.3.0 is released. The release notes can be viewed at https://github.com/

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Cumulus 2.3.0 is released

Hello All, Cumulus version 2.3.0 is released. The release notes can be viewed at https://github.com/

10/31/22

Jackson Smith, … Yiming Yang27

10/25/22

Terra workflow exiting with "invalid return code 1"

Dear Yiming and Bo, Thank you so much for your help with this. I greatly appreciate you taking the

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Terra workflow exiting with "invalid return code 1"

Dear Yiming and Bo, Thank you so much for your help with this. I greatly appreciate you taking the

10/25/22

Wesley Kwong, Bo Li2

10/13/22

Does cumulus support cellranger multiomics between gene expression and vdj?

Hi Wesley, No. Currently cellranger_multi only supports assays with CMO. Best, Bo Bo Li, Ph.D.

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Does cumulus support cellranger multiomics between gene expression and vdj?

Hi Wesley, No. Currently cellranger_multi only supports assays with CMO. Best, Bo Bo Li, Ph.D.

10/13/22

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