Seqera containers: POC 2

[ewels]

Seqera Containers: Proof of concept No. 2

Generate containers at user-download

Workflow for generating:

• Nothing. Container is stripped from pipeline, so just update conda.

Workflow for usage:

• Online
  • Use nextflow run -profile seqera_containers (-profile seqera_containers,singularity, -profile seqera_containers,singularity,arm etc)
• Offline
  • Download process (could be bundled into a single command at later date). Something like:

    nf-core download seqeralabs/nf-aggregate
    nextflow inspect . -concretize -profile test,seqera_containers,singularity > containers.json
    jq -r '.processes[].container' containers.json | sort | uniq > containers.txt
    while IFS= read -r line; do singularity pull "$line"; done < "$1"

  • Generate a local config file to tell Nextflow where to find the Singularity image files. eg:

    nextflow inspect . -concretize -profile test,seqera_containers,singularity -format config > containers.config
    # Manually switch out base file path with downloaded filenames, I guess?

  • Would need documentation and ideally addition to the nf-core download command.

[edmundmiller]

How confident in the Wave service uptime are you?

The Wave API has an outage and it's quay.io flaking out all over again.