nf-core_pipelines

nf-core_pipelines.md

nf-core

rnaseq

• don't use one large container b/c of maintenence and modularity
• if conda installs, use conda directly
• good usage example
• good versioning example tool or container level? self documenting containers?
• good output template
• good pipeline wrapper
• no pipeline rule sharing
• common pipeline template

singularity

Singularity runs on all CHOP machines

• module load singularity
• respublica node support

Singularity does not run on macs

• singularity+snakemake docker container can run singularity in docker on macs

Singularity images do not always update for snakemake

• Dockerhub updates are not always applied for snakemake
• Delete the snakemake simg file, and try a different machine

You can package data with tools

• Dockerhub has no container size limit

Images are difficult to debug

• Local experementation requires a lot of disk space
  • mac has disj space bug
  • chop machines have little docker space
• Dockerhub builds are slow

snakemake does not support tags/versions