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.