Unable to run sarek workflow in AWS health omics

DimitrisZisis commented 7 months ago

Description of the bug

I was following the tutorial https://catalog.us-east-1.prod.workshops.aws/workshops/76d4a4ff-fe6f-436a-a1c2-f7ce44bc5d17/en-US/workshop/test-workflow and I managed to create my workflow in AWS Helathomics. Everything is correctly done but when I am trying to run the workflow in healthomics it is not working
I am receiving strange kinds of errors related to the input parameters or samplesheet.I changed the parameters and I removed the -- so now I am getting the following. Do you have any idea what can be wrong?

Command used and terminal output

WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config
WARNING: Could not load nf-core/config/sarek profiles: https://raw.githubusercontent.com/nf-core/configs/master/pipeline/sarek.config
Launching `sarek/main.nf` [prickly_mirzakhani] DSL2 - revision: 48ed053221
Module path must start with / or ./ prefix -- Offending module: plugin/nf-validation,  -- Check script 'sarek/main.nf' at line: 79 or see '.nextflow.log' file for more details
Nextflow engine failed

Relevant files

No response

System information

No response

asp8200 commented 7 months ago

@DimitrisZisis : Thanks for reporting this. I know that Sarek runs fine over awsbatch, so I guess it should also be possible to get it running over AWS Healthomics.

Did you manage to get through the tutorial using scrnaseq?

I suggest that you come on over on nf-core's Slack channel for Sarek, and we can try to see if we can help you. Cheers

DimitrisZisis commented 7 months ago

Yes i followed all the steps of the tutorial for scrnaseq I did exactly what they described but at this point, I have this error. It seems to have a problem with plugin/nf-validation but I don't know why. Do you think that this can be related to IAM role? apart from the zip and what is described in the tutorial is it necessary to upload something else in Healthomics ?

Regarding Slack channel, i tried to register and get connected but it is impossible. They support only 2 channels (seqera.io and pbic...) and Google doesn't work!

asp8200 commented 7 months ago

https://nfcore.slack.com/channels/sarek

FriederikeHanssen commented 7 months ago

@DimitrisZisis internally propagated and someone will fix the slack link. Sorry about that. There is a amazon-healthomics channel on slack that would be a good place to ask.

DimitrisZisis commented 7 months ago

Yes but the above link and any other connection link doesn't work. I can't get the 6 digits code in my email.

DimitrisZisis commented 7 months ago

after carebully testing sarek on my computer, it seems that one of the problems is the version of nextflow that AWS healthomics uses. I installed the same version (version 22.04.0) and I get an error about the same nf-validation plugin.

N E X T F L O W  ~  version 22.04.0
Launching `[https://github.com/nf-core/sarek`](https://github.com/nf-core/sarek%60) [spontaneous_kowalevski] DSL2 - revision: 6aeac929c9 [3.4.0]
Cannot find the latest version of nf-validation plugin

I tried manually to install other versions of nf-validation plugin but all versions require nextflow > 22.1.0. So it seems that the nextflow version in AWS health omics should be nextflow > 22.1.0 and now is 22.04.0.

FriederikeHanssen commented 7 months ago

Slack link was fixed

DimitrisZisis commented 7 months ago

Sorry but in my case doesn't work. i add my email and I received instead of 6 digits password an email saying no account found. Can you send me another link?

FriederikeHanssen commented 7 months ago

Did you press 'Join' in the top right corner? https://nf-co.re/

DimitrisZisis commented 7 months ago

Yes, i did !!! In the section Slack if you click on get an invite button, connection with google or apple doesn't work and the email section supports only accounts with domains : qbic.uni-tuebingen.de, seqera.io. if you enter your email and click send verification code an email will come with "It looks like there isn’t an account on nf-core tied to this email address"

FriederikeHanssen commented 7 months ago

@mribeirodantas can you check what is going on there?

DimitrisZisis commented 7 months ago

someone fixed it and i am able to connect ! Thank you! Lets see if we will solve the real problems related to nf-core and AWS healthomics. One basic problem I ve noticed is that the AWS uses a very old version of Nextflow

FriederikeHanssen commented 4 months ago

Is this resolved?

nf-core / sarek