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    James A. Fellows Yates
    @jfy133
    (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
    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
    Nextflow Tower 8-24-2021 9-07-41 AM.png
    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 :)
    Phil Ewels
    @ewels
    Would be nice if Tower had an equivalent of ~/nextflow/config
    eg. A config that is always applied for every launch
    (After Tower defaults 😉)
    Bryan Lajoie
    @bryanlajoie_twitter
    ^ yes please !
    Phil Ewels
    @ewels
    @pditommaso nothing wrong with it per se, just no way to have a default that takes priority over Tower defaults. So for stuff like this you have to manually enter a specific config in the UI for every launch.
    Is there a place to see the default config that Tower gives Nextflow?
    Bryan Lajoie
    @bryanlajoie_twitter
    Why wouldn't user/pipeline conf always come last, to have the ability to override anything and everything?
    Phil Ewels
    @ewels
    I guess so that Tower can "make stuff work" on cloud etc. But yeah I guess most pipelines don't set these things so in majority of cases the order would have no effect.
    Bryan Lajoie
    @bryanlajoie_twitter
    agreed, so for now, perhaps tower should only set things that the user would never to tweak. Later change around the ordering to give the user full control?
    As a workaround, we've added the necessary aws tweaks to the launchpad default nextflow-config options. Re. uploadChunkSize, it may be better for tower/nf to use a dynamically set chunksize by default. Basespace cli does similar I believe.
    As is, tower has a limit of 100gb via the 10mb default.