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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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nextflow inspect does not work due to missing parameters #347

Open stevekm opened 1 month ago

stevekm commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

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