Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

nextflow inspect does not work due to missing parameters #347

Open
stevekm opened this issue Jul 26, 2024 · 2 comments
Open

nextflow inspect does not work due to missing parameters #347

stevekm opened this issue Jul 26, 2024 · 2 comments
Labels
bug Something isn't working

Comments

@stevekm
Copy link

stevekm commented Jul 26, 2024

Description of the bug

I am trying to programmatically get the list of all containers in the pipeline. However the standard command nextflow inspect does not seem to work, even if you tell it to ignore errors.

nextflow inspect "https://github.com/nf-core/scrnaseq" -r "master" -ignore-errors
ERROR ~ ERROR: Validation of pipeline parameters failed!


The following invalid input values have been detected:

* Missing required parameter: --input
* Missing required parameter: --outdir

Any ideas how to fix this? Ideally in a manner that will work for all pipelines, and not just scrnaseq, since I will be using the same method to get the list of containers from all pipelines running in the Nextflow Tower instance.

@robsyme you might be interested in this one also

Command used and terminal output

No response

Relevant files

No response

System information

nextflow version 24.04.2.5914

@robsyme
Copy link
Contributor

robsyme commented Jul 26, 2024

I'd recommend adding -profile test,docker. This will solve at least the --input parameter and will ensure that nextflow inspect returns you docker images. This is the default, but there is no harm in being explicit.

Almost all nf-core workflows will only then require --outdir which you can set to an arbitrary directory that can be deleted afterwards.

@robsyme
Copy link
Contributor

robsyme commented Jul 26, 2024

What is the ignore-errors parameter? I don't think I've seen that before.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

2 participants