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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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Unable to pull from repository #94

Closed llk578496 closed 1 year ago

llk578496 commented 1 year ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v0.3.30

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow pull epi2me-labs/wf-artic

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

Hi, we just tried to update the wf-artic by using the above command but seems it fails. May we seek your help? Thank you.

Relevant log output

(nextflow) gilman_siu2@gilmansiu2-Z490-VISION-D:/mnt/data6/COVID$ nextflow pull epi2me-labs/wf-artic
Checking epi2me-labs/wf-artic ...
epi2me-labs/wf-artic contains uncommitted changes -- cannot pull from repository

Application activity log entry

No response

mattdmem commented 1 year ago

Hello @llk578496,

This sometimes happens if you have changes in the previously pulled version of the workflow.

This is usually located in:

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

Try deleting this directory if it exists and try nextflow pull again. Let me know if this works.

You could also try pulling the specific versions which you would like by specifying -r - further details here: https://www.nextflow.io/docs/latest/cli.html#pull

Thanks

Matt

llk578496 commented 1 year ago

It works. Thanks a lot.