GenPipes

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Welcome to the GenPipes (C3G analysis pipelines) mailing list.

Here you can find questions and answers or comments on our pipeline suite.

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May 1

Release of GenPipes 4.6.0

A new release of GenPipes, 4.6.0 is now available. What's new? ========== This is a medium

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Release of GenPipes 4.6.0

A new release of GenPipes, 4.6.0 is now available. What's new? ========== This is a medium

May 1

Feb 9

Release of GenPipes 4.5.0

A new release of GenPipes, 4.5.0 is now available. What's new? ========== This is a medium

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Release of GenPipes 4.5.0

A new release of GenPipes, 4.5.0 is now available. What's new? ========== This is a medium

Feb 9

Jan 8

Release of GenPipes 4.4.5

A new release of GenPipes, 4.4.5 is now available. What's new? ========== This is a bug-fix minor

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Release of GenPipes 4.4.5

A new release of GenPipes, 4.4.5 is now available. What's new? ========== This is a bug-fix minor

Jan 8

9/11/23

Release of GenPipes 4.4.4

A new release of the GenPipes, 4.4.4 is now available. What's new? ========== This is a bug-fix

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Release of GenPipes 4.4.4

A new release of the GenPipes, 4.4.4 is now available. What's new? ========== This is a bug-fix

9/11/23

8/24/23

Release of GenPipes 4.4.3

A new release of the GenPipes, 4.4.3 is now available. What's new? ========== This is a bug-fix

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Release of GenPipes 4.4.3

A new release of the GenPipes, 4.4.3 is now available. What's new? ========== This is a bug-fix

8/24/23

6/21/23

Release of GenPipes 4.4.2

A new release of the GenPipes, 4.4.2 is now available. What's new? ========== This is a bug-fix

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Release of GenPipes 4.4.2

A new release of the GenPipes, 4.4.2 is now available. What's new? ========== This is a bug-fix

6/21/23

Nawal Chehab, Alain Pacis2

5/11/23

ChIP model peak and change mfold

Hi Nawal, Thanks for your message. Would it be possible to send me a UCSC track link (if available)

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ChIP model peak and change mfold

Hi Nawal, Thanks for your message. Would it be possible to send me a UCSC track link (if available)

5/11/23

James Saliba, … José Héctor Gálvez9

4/29/23

Hi Jose, Thank you for your detailed response, it was very illuminating! Best, James On Thursday,

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Hi Jose, Thank you for your detailed response, it was very illuminating! Best, James On Thursday,

4/29/23

James Saliba, Mareike Janiak3

4/25/23

blacklisted chip regions

Sounds great thanks! On Tuesday, April 25, 2023 at 10:10:47 AM UTC-4 mareike...@computationalgenomics

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blacklisted chip regions

Sounds great thanks! On Tuesday, April 25, 2023 at 10:10:47 AM UTC-4 mareike...@computationalgenomics

4/25/23

edouard.henrion

3/14/23

Release of GenPipes 4.4.1

A new release of the GenPipes, 4.4.1 is now available. What's new? ========== This is a bug-fix

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Release of GenPipes 4.4.1

A new release of the GenPipes, 4.4.1 is now available. What's new? ========== This is a bug-fix

3/14/23

edouard.henrion

3/9/23

Release of GenPipes 4.4.0

A new release of the GenPipes, 4.4.0 is now available. What's new? ========== This is a medium

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Release of GenPipes 4.4.0

A new release of the GenPipes, 4.4.0 is now available. What's new? ========== This is a medium

3/9/23

edouard.henrion

12/8/22

Release of GenPipes 4.3.2

What's new? ========== This release is mainly a bug-fix release : * Tumor Pair : fixed '

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Release of GenPipes 4.3.2

What's new? ========== This release is mainly a bug-fix release : * Tumor Pair : fixed '

12/8/22

Shraddha Pai, … edouard.henrion6

10/26/22

GenPipes on Graham: no module named configparser

Thanks Edouard, that worked. The pipeline ran from end to end and I am able to see the output files.

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GenPipes on Graham: no module named configparser

Thanks Edouard, that worked. The pipeline ran from end to end and I am able to see the output files.

10/26/22

edouard.henrion, … Shraddha Pai4

10/18/22

Release of GenPipes 4.3.1

Hi Edouard, Great, I see it now. Thank you also for the documentation website. I will follow the

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Release of GenPipes 4.3.1

Hi Edouard, Great, I see it now. Thank you also for the documentation website. I will follow the

10/18/22

kathlee...@gmail.com, edouard.henrion2

10/7/22

Compute Canada GenPipes Version

Hi Kathleen, Yes GenPipes 4.3.1 is out ! Sorry I didn't post the message in the forum, by mistake

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Compute Canada GenPipes Version

Hi Kathleen, Yes GenPipes 4.3.1 is out ! Sorry I didn't post the message in the forum, by mistake

10/7/22

Michele Tinti, José Héctor Gálvez2

9/30/22

tumor pair pipline question

Hello Michele, While it is indeed possible to use the pipeline for the application you describe, it

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tumor pair pipline question

Hello Michele, While it is indeed possible to use the pipeline for the application you describe, it

9/30/22

edouard.henrion

6/15/22

GenPipes release 4.3.0

A new release of the GenPipes, 4.3.0 is now available. What's new? ========== * MethylSeq :

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GenPipes release 4.3.0

A new release of the GenPipes, 4.3.0 is now available. What's new? ========== * MethylSeq :

6/15/22

edouard.henrion

6/2/22

GenPipes release 4.2.0

A new release of the GenPipes, 4.2.0 is now available. What's new? ========== * New ini file

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GenPipes release 4.2.0

A new release of the GenPipes, 4.2.0 is now available. What's new? ========== * New ini file

6/2/22

José Héctor Gálvez

5/30/22

GenPipes User Survey

Hello GenPipes users, As part of our planning for future development, we would appreciate it if you

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GenPipes User Survey

Hello GenPipes users, As part of our planning for future development, we would appreciate it if you

5/30/22

Marco, GenPipes3

2/19/22

genpipes/4.1.2 Error

Hello ... Thanks for that suggestion. It worked, one step further. But now I am getting this error ..

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genpipes/4.1.2 Error

Hello ... Thanks for that suggestion. It worked, one step further. But now I am getting this error ..

2/19/22

Neha Joshi, Pubudu Nawarathna2

10/26/21

creating a custom reference.ini

Hi, What is the genome you want to use? First we have to check whether the genome is already stored

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creating a custom reference.ini

Hi, What is the genome you want to use? First we have to check whether the genome is already stored

10/26/21

10/1/21

Incompatible genomes for RNA-seq

Hello, I am currently trying to run the genpipes RNA-seq pipeline (version 3.6.0) on the beluga

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Incompatible genomes for RNA-seq

Hello, I am currently trying to run the genpipes RNA-seq pipeline (version 3.6.0) on the beluga

10/1/21

5/25/21

Good morning, I see that you have switched to skewer in your DNA seq pipeline. Can you help me

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Good morning, I see that you have switched to skewer in your DNA seq pipeline. Can you help me

5/25/21

edouard.henrion

5/4/21

GenPipes release 3.4.0

A new release of the GenPipes, 3.4.0 is now available. What's new? ========== * Major update of

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GenPipes release 3.4.0

A new release of the GenPipes, 3.4.0 is now available. What's new? ========== * Major update of

5/4/21

gona.s...@gmail.com

3/12/21

DNAseq not detecting completed jobs using containerized version of genpipes

Hello. I am running genpipes from a container on an external SLURM cluster. This involves use of the

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DNAseq not detecting completed jobs using containerized version of genpipes

Hello. I am running genpipes from a container on an external SLURM cluster. This involves use of the

3/12/21

Édouard Henrion

2/22/21

GenPipes release 3.3.0

A new release of the GenPipes, 3.3.0 is now available. What's new? ========== * 2 steps added in

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GenPipes release 3.3.0

A new release of the GenPipes, 3.3.0 is now available. What's new? ========== * 2 steps added in

2/22/21

GenPipes, Shaloo Shalini2

2/11/21

GenPipes release 3.2.0

Latest GenPipes release 3.2.0 documentation is now available for reference here: https://genpipes.

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GenPipes release 3.2.0

Latest GenPipes release 3.2.0 documentation is now available for reference here: https://genpipes.

2/11/21

Anjani Nair, Shaloo Shalini3

12/28/20

Contributing to the codebase

Thanks! On Mon, 28 Dec 2020, 12:19 Shaloo Shalini, <shaloo....@gmail.com> wrote: Hi Anjani,

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Contributing to the codebase

Thanks! On Mon, 28 Dec 2020, 12:19 Shaloo Shalini, <shaloo....@gmail.com> wrote: Hi Anjani,

12/28/20

12/2/20

I am looking for someone to walk me through the snp calling pipeline for an in house genome. I'm

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I am looking for someone to walk me through the snp calling pipeline for an in house genome. I'm

12/2/20

franc...@gmail.com

11/14/20

chip-seq pipeline mark duplicates

I am trying to run the chip-seq pipeline and am not able to get past the mark duplicates step. i am

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chip-seq pipeline mark duplicates

I am trying to run the chip-seq pipeline and am not able to get past the mark duplicates step. i am

11/14/20

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