The ‘Maintainers Minutes’ aims to further give insight into the workings of the nf-core maintainers team by providing brief summaries of the monthly team meetings.
Batch modules update
Seqera Containers
Phil Ewels joined us to chat about migrating to Seqera Containers which ties into the batch modules update we have been discussing in the last few months. We agreed on a general structure and refactoring plan to incorporate the new container repository as well as leveraging conda lock files for better reproducibilty. Phil and Edmund Miller will put together blog posts describing the plan in detail.
Renovate
We also voted on the structure of the environment.yml’s generated by renovate and decided to keep the explicit channel declaration to safe-guard against any accidental package name duplication across multiple channels:
channels:
- conda-forge
- bioconda
dependencies:
# renovate: datasource=conda depName=bioconda/bwa
- bioconda::bwa=0.7.18
# renovate: datasource=conda depName=bioconda/samtools
- bioconda::samtools=1.20
# renovate: datasource=conda depName=bioconda/htslib
- bioconda::htslib=1.20.0Testing
In the previous meeting we discussed a more comprehensive testing strategy. As a result we decided that in addition to a docker based test, also singularity and conda should be run on a PR made to the master branch.
Júlia Mir added this now to tools and it will be rolled out with the next template update.
Office Hours
Earlier this year, we tried out “office hours”. We reviewed its reception and decided to continue it under a new name. More details following soon.
Expand modules guidelines
Simon Pearce suggests to change the guidelines of the default prefix for modules. The advantage would be that
many developers do it by default when submitting a module already and the likelihood of a module working without any additional configuration is higher.
Counter arguments are that we are just kicking the can down the road: it is still easy to generate output files with the same suffix (i.e. sorted.bam).
One idea is, to add the task name as default which is long and ugly. The newly proposed output definition will alleviate some of these pain points as well.
Please review Simon’s PR above, if you want to weigh in on the discussion.
Update documentation
We noticed that the nf-test assertions page is in need of updating. Maxime Garcia will take the lead in that pinging people as needed.
- ❤️ from your #maintainers team!
