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[Bug]: nextflow run epi2me-labs/wf-cnv not work in docker container ontresearch/wf-cn #3

Open gudedsh opened 1 month ago

gudedsh commented 1 month ago

What happened?

I am trying to use the docker container ontresearch/wf-cn or ontresearch/wf-human-variation, but it did not work, the error as below: bash: nextflow: command not found

Operating System

ubuntu 20.04

Workflow Execution

EPI2ME Labs desktop application

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - CLI Execution Profile

None

Workflow Version

ontresearch/wf-human-variation

Relevant log output

bash: nextflow: command not found
cjw85 commented 1 month ago

These containers are used by our workflows, they do not contain nextflow because they do not need to.

SamStudio8 commented 1 month ago

Hi @gudedsh, wf-cnv is a deprecated workflow and you'll probably be wanting to look at wf-human-variation (https://github.com/epi2me-labs/wf-human-variation) instead.

Your problem report says you are using the EPI2ME Desktop application but I'm not sure that is the case from your log output. Can you provide some more information on what command you ran on the command line and what you expected to happen? It looks as though you might be trying to run Nextflow from inside one of our workflow containers, note that these containers are launched by running our Nextflow workflows (and so do not need to include Nextflow).