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Paolo Di Tommaso

@pditommaso

we are discuss internally how to evolve the OSS project in a more sustainable manner

Andrew Birnberg

@birnbera

@pditommaso and @ewels thanks for the information. Sharing an account is fine for us, but the problem is that multiple people can't login with the same account simultaneously. @pditommaso do you know how hard it would be disable this restriction?

Paolo Di Tommaso

@pditommaso

but the problem is that multiple people can't login with the same account simultaneously

why not? I'm not aware of this limitation

5 replies

varun171

@varun171

Can someone suggest how to run a pipeline with a specific version of nextflow from nf-tower?

Phil Ewels

@ewels

You can't, I believe

Pretty sure that tower is locked to a specific version, when launching at least

(Maaaybe this is only AWS? Not sure?)

varun171

@varun171

Ok Thanks Phil.

James A. Fellows Yates

@jfy133

Is it possible to monitor CLI executed runs of multiple users in an organisation/workspace on the Seqera hosted Tower? Currently my token shares monitoring info with my own user workspace, but not to the organisation - how would I make it so info is sent to the organisation instead?

The message on the Runs tab of the workspace says either launch a job from tower (which isn't possible in this case), or check the following documentation: https://tower.nf/welcome Yet this is for single users? I also don't see any information for CLI executed runs on help.tower.nf either....

(unless this is what Tower OSS is referring to in the discussion above...)

Or are organisations/workspaces only actually for launching jobs?

Paolo Di Tommaso

@pditommaso

yes, you need to specify the workspace id, either via TOWER_WORKSPACE_ID env var or tower.workspaceId in the nextflow.config

6 replies

Edmund Miller

@e_miller_gitlab

Hello all! Is there any way to get tower to configure the VPC? Unable to find default AWS subnets for vpc none and region us-west-2 when I left it blank. When I fill it out with the default VPC our devops group set up the tower head CE fails with

INVALID - CLIENT_ERROR - Your compute environment has been INVALIDATED and scaled down because none of the instances joined the underlying ECS Cluster. Common issues preventing instances joining are the following: VPC/Subnet configuration preventing communication to ECS, incorrect Instance Profile policy preventing authorization to ECS, or customized AMI or LaunchTemplate configurations affecting ECS agent.

gq7f041p

@gq7f041p_twitter

Hi all, is there a way to pull docker images from a private docker repo to use for nextflow processes? Curious if there's a way to add docker credentials (or log into docker) on tower.nf or is there's another way to do this.

Phil Ewels

@ewels

@gq7f041p_twitter - you can set a private Docker registry in Nextflow: https://www.nextflow.io/docs/latest/config.html#config-docker - not sure if that does what you're looking for?

1 reply

Edmund Miller

@e_miller_gitlab

I don't think that would have the private registry credentials is the issue

Phil Ewels

@ewels

@jfy133 (is it you? Gitter mobile app is crap and not showing the user) I documented the workspace ID stuff the other day for the NF-core action thing: https://github.com/nf-core/tower-action#workspace_id

4 replies

Paolo Di Tommaso

@pditommaso

Is there any way to get tower to configure the VPC?

when configuring the Tower CE specify the VPC you want to use in the advanced options

6 replies

jamesbaye

@jamesbaye

I have a few runs that I interrupted but that still appear as ongoing in tower (blue colour, greyed delete button). How might I delete them from the tower interface?

Paolo Di Tommaso

@pditommaso

it should go into unknown status after a while, then you should be able to delete them

5 replies

let us know if the problem persists

luantunez

@luantunez

Hi! I am not being able to run Netxflow Tower with the Sarek pipeline

I am not sure about the proble, but could it be the parameters file? I am writing

{“input”:  "/fusion/s3/s3-gnf-02/demo01/sample.tsv”,
    “genome”:  “GRCh38”}

4 replies

also, this directory is not being created in my S3 bucket

Staging foreign file: /.nextflow/assets/nf-core/sarek/docs/images

Please help :)

Phil Ewels

@ewels

Parameters file is the same as -params-file so should be valid JSON or YAML

So you can run your file through a JSON validator online

luantunez

@luantunez

Thank you for your response! It is taking the json though, but I think the parameters are not ok, maybe because it is not downloading the /.nextflow folder in my S3 bucket?

kaitlinchaung

@kaitlinchaung

Hi everyone! Apologies in advance if this isn't the best place to ask, but is anyone else having issues loading tower after the Chrome update[Version 92.0.4515.131 (Official Build) (x86_64)]?
I am able to access tower via Safari or my mobile Chrome browser(Version 92.0.4515.90)

Paolo Di Tommaso

@pditommaso

I'm using 92.0.4515.131 and I've seen any problem, can you provide more detail regarding the issue?

3 replies

Viren Amin

@virenar

Is there a way to specify which version of the nextflow to use in the nextflow tower when launching the pipeline through the launchpad? Currently, it uses edge release and wanted to use a stable version.

Phil Ewels

@ewels

I think this has been asked before and the answer was no.

Viren Amin

@virenar

Thanks @ewels will keep using cli then

Matthieu Pichaud

@MatPich_twitter

Hi guys, have you encountered this error before?
No such property: inittag for class: Script_c812b1e6
It stops the workflow before anything is run.
Thanks for your help!

Paolo Di Tommaso

@pditommaso

please fill-out an issue including the nextflow log file

https://github.com/seqeralabs/nf-tower

Bryan Lajoie

@bryanlajoie_twitter

Using nf + tower + aws-batch. Blocked due to the default aws uploadChunkSize default of 10mb, which limits file size to 100G. No matter where I change this param (base.conf, nextflow.config, etc) it seems to always revert to the default of 10485760 via the tower 'resolved configuration'.

uploadChunkSize = 10485760

If I however enter this conf change into the UI manually, via the launch / nextflow config file option, then it does stick in the workflow resolved configuration. Any ideas?

2 replies

Paolo Di Tommaso

@pditommaso

yes, tower defaults that attributes to 10 MB

Phil Ewels

@ewels

I think that the config parsing goes pipeline, then tower defaults, then UI inputs

So if it's something that Tower sets as a default, it's not something that you can ever affect from the pipeline code / config

And there is no way around this that I know of..(?)

Paolo Di Tommaso

@pditommaso

I think that the config parsing goes pipeline, then tower defaults, then UI inputs

exactly, what's wrong with that?

Bryan Lajoie

@bryanlajoie_twitter

I'd like to ideally set that param in the pipeline config, and not have tower override my set chunk size.

Can I somehow set that UI option via api? I can't be setting this manually for every launch :)

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