You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
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.
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.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
The text was updated successfully, but these errors were encountered: