Just 15 minutes + questions, we focus on topics about using and developing nf-core
pipelines. These are recorded and made available at https://nf-co.re
, helping to build an archive of training material. Got an idea for a talk? Let us know on the #bytesize
Slack channel!
With the advent of DSL2, nf-core pipelines began to use separate containers for every process. Now, many nf-core pipelines can have upwards of 50 different software containers in a single run. Traditionally, finding the URIs for each of these containers was a difficult task, with several people developing tooling based around regular expressions.
In Nextflow 23.09.0-edge a new subcommand was added called nextflow inspect.
This command retrieves all of the containers that will be used by a pipeline run and returns them in Nextflow config syntax.
In this talk, Phil Ewels (@ewels) will guides us through the process of fetching container URIs using nextflow inspect
and show how this can be used to customise containers in a pipeline. This may be of particular use to people working in environments that cannot
access our public container registries or who may need additional steps in their container verification steps.
Unfortunately, the recordings for this bytesize was corrupted. Some of the content, however, was repeated in the bytesize Bytesize: Explaining Wave containers.