Dependencies containerized

How to get containers used by nf-core pipelines

(nextflow version 24.10.4.5934)

Option 1: Nextflow inspect

Documentation:
Bytesize: Explaining Wave containers (Minute 22+)
https://www.nextflow.io/docs/latest/reference/cli.html

Nextflow inspect provides an overview of processes, but it seems to required “dummy” input/outout definitions (Could this be solved in new version).

Here an example:
nextflow inspect nf-core/sarek -profile test,singularity --outdir dummy

Output is json and can easily be parsed, e.g., via python or jq.

Limitations/Questions:

1. Only containers of processes executed with the corresponding “run” command are included.
2. Requires running nextflow.

Option 2: Parse from github repo files

Each nf-core pipeline repo has a modules folder and each (?) module should contain a container line showing the information on container used.

Here is how it looks:

    conda "${moduleDir}/environment.yml"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data':
        'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }"

Parsing via grep should be no problem.

Limitations/Questions:

1. Does this cover all container used?
2. Would this be possible without download the repo first.

Start by comparing Nextflow inspect output for the example nf-core/sarek command with container declarations in the pipeline's modules folder. Determine whether the modules cover all containers and whether extraction can work without downloading the repository; done should document the supported approach and its limitations.