search

epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
Other
47 stars 34 forks source link

[Bug]: Unable to pull #57

Closed leoncaly closed 2 years ago

leoncaly commented 2 years ago

What happened?

After running nextflow nextflow indicated N E X T F L O W ~ version 22.04.0 NOTE: Your local project version looks outdated - a different revision is available in the remote repository

When running running nextflow pull epi2me-labs/wf-artic the resultant output is epi2me-labs/wf-artic contains uncommitted changes -- cannot pull from repository

Operating System

ubuntu 20.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - Execution Profile

Conda

Workflow Version

N E X T F L O W ~ version 22.04.0

Relevant log output

After running nextflow nextflow indicated
N E X T F L O W  ~  version 22.04.0
NOTE: Your local project version looks outdated - a different revision is available in the remote repository

When running running nextflow pull epi2me-labs/wf-artic the resultant output is epi2me-labs/wf-artic contains uncommitted changes -- cannot pull from repository
mattdmem commented 2 years ago

Hi @leoncaly - did you alter your local code in any way?

You could try and delete your nextflow cache - do you have this folder:

~/.nextflow/assets/epi2me-labs/wf-artic

If so delete it and try again - let me know how you get on.

Matt

leoncaly commented 2 years ago

Greetings Matt,

I haven’t altered local code in any way. I am seeing the same issue across 2 different Ubuntu machines as well as my MacOS machine.

On one of my Ubuntu machines I removed the wf-artic folder as instructed below.

I then receive

Checking epi2me-labs/wf-artic WARN: Cannot read project manifest — Cause api-github.comhttp://api-github.com Cannot find ‘epi2me-labs/wf-artic — Make sure exists a GitHub repository at this address ‘https://github.com/epi2me-labs/wf-artic'

Dr. Leon Caly Adjunct Senior Research Fellow, Monash University Deputy High Containment Facility Manager Translational Diagnostics Laboratory Victorian Infectious Diseases Reference Laboratory | www.vidrl.org.auhttp://www.vidrl.org.au Doherty Institute | www.doherty.edu.auhttp://www.doherty.edu.au 792 Elizabeth Street, Melbourne, 3000.

Phone# +61-3-9342-9678 Fax# +61-3-9342-9629 Email: @.**@.>

@.*** Email tone can be misinterpreted, please read my email with warmth and good intentions.

On 20 Jul 2022, at 5:53 pm, Matthew Parker @.**@.>> wrote:

Hi @leoncalyhttps://secure-web.cisco.com/15W_2Uc-uRec12xxrje7mp4Wy1RrZ-j_jyNQAFxHvQDMWyCO6RKgV11OqWNcksZCoXH8V4y9dgXNSZ0WtCpxdgAeyjwU7dr5tyIQCHvTsr95EY8SPQPNhlXrFMFWVXXetkPZ8E5y7AWql74_2Qd2Y5VdXQbH9auta-N0HvRU44FCA_w0eAQpmHNVJLVpw6pVWVK6IH5olR-ylxshSr1t60SyULySFGu7Ups1RHJ67t2Ld2S-I_cq1C67pYqkQfNVjeH8jwD-y5nCA5fyIIgM3JX4QJ0ND_ABWdpYsb1Q6aziXyhxHyV5Wlfj-xJMNmbq9/https%3A%2F%2Fgithub.com%2Fleoncaly - did you alter your local code in any way?

You could try and delete your nextflow cache - do you have this folder:

~/.nextflow/assets/epi2me-labs/wf-artic

If so delete it and try again - let me know how you get on.

Matt

— Reply to this email directly, view it on GitHubhttps://secure-web.cisco.com/1_Zx2nNnk-oC9GCUC2ET0aY3dtLZTbKT344bRQZzefumaKLiddv5lhSSHBSPmZfXE2Ripm13vzg60gU41UKYd-n2DWoMfdPWI1ooMDXKkJB5OEHkhmiJ_4fHF6ssiVciim1sMGlN9-vAQlXzPmJWxL6d_H5mjTbz8QwbyFzSOg6ZgUMZ1_lnAIeVoOc2yF68COD3TgG4chuV3_Fvt1vrd9YK8wpce31zgWfkMes8vIHk3SI6XtQDrdqC7LK7bzd_u_8mQYEWeugEZk5oFK8mHS6nWsm3k53nxXl76GEolkYlN2ef26iYNVCCWR3HSJ1Ad/https%3A%2F%2Fgithub.com%2Fepi2me-labs%2Fwf-artic%2Fissues%2F57%23issuecomment-1189948995, or unsubscribehttps://secure-web.cisco.com/1x0FDwbtrUQe2pnatBsrv3LiDn21RS6wOXKl6TPD71vZHTfLjXHfNWGFtIX7uCVRqHc6aFK_tm-KIpGNFHtvUlzpBwj2ZZNa--7LOTXTIkt1dvk2wZ4g5GzhsbayePPn2j18sOO6i9Rr89n4fsSZWLcBKt9HnYbar3W3ZWCbLDF0hHVxxjZDpSF1xibf5AVp5lzahjcPuIaOD13YElhU0M68wYnVDvCF6ySgUT0UGbnNxONf4p8m9Xb9I0W29R3_nZ-pXtiNJIXrubhigyaaIyIlBglJajtktDMK7JyAE5v4q4nVO7wLXNEy9z1kX6eCw/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALUF7BTFHF4ZNRDPOZQCDCDVU6WBDANCNFSM54BGYDVQ. You are receiving this because you were mentioned.Message ID: @.***>

WARNING: This message originated from outside the Northern/Melbourne/Western Health e-mail network. The sender cannot be validated. Caution is advised. Contact IT Services for more information.

mattdmem commented 2 years ago

@leoncaly we cannot reproduce the problem internally so we're wondering if its some network configuration issue at your institution? We also sometimes encounter problems if we hit the GitHub API from the same IP address multiple times. It would be good to check if you see the same problem on another network?

Thanks

Matt

leoncaly commented 2 years ago

@mattdmem I have tried 3 different networks including hotspot via mobile phone and all 3 systems bring up the same error (Ubuntu 22, Ubuntu 20 and MacOS 12.5). All systems are running conda 4.1.3 I have created a new nextflow env and still see the same error.

UPDATE: I removed nextflow env and ~/.nextflow/ entirely on all systems. Reinstalled and now everything appears to be working. I'm not entirely sure what caused this to occur but at least everything is working now.

Thank you.

mattdmem commented 2 years ago

Thanks for the update and glad you are up and running!