/wdl-list-versions

Primary LanguagePythonEuropean Union Public License 1.2EUPL-1.2

wdl-list-versions

Dump out the versions of containers imported in a WDL workflow.

The original version of this tool tried to guess exactly which tasks were called, but this had some issues, so now we just walk the entire import tree.

MultiQC

This is for use in a multiqc.yaml report.

$ wdl-list-versions methylasso.wdl
software_versions:
  containers:
    ghcr.io/biowdl/docker-methylasso:
    - main
    quay.io/biocontainers/bedtools:
    - 2.30.0--h7d7f7ad_2
    - 2.23.0--hdbcaa40_3
    - 2.31.1--hf5e1c6e_2
    quay.io/biocontainers/samtools:
    - 1.21--h96c455f_1
  miniwdl:
    miniwdl: v1.13.0
    miniwdl-slurm: 0.4.1.dev8+g54512d7


$ wdl-list-versions methylasso.wdl  --by-task
software_versions:
  containers:
    Awk:
    - quay.io/biocontainers/samtools:1.21--h96c455f_1
    MethyLasso:
    - ghcr.io/biowdl/docker-methylasso:main
    bedtools.Complement:
    - quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3
    bedtools.Coverage:
    - quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2
    bedtools.Intersect:
    - quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2
    bedtools.Merge:
    - quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3
    bedtools.MergeBedFiles:
    - quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3
    bedtools.Sort:
    - quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2
  miniwdl:
    miniwdl: v1.13.0
    miniwdl-slurm: 0.4.1.dev8+g54512d7

JSON

$ wdl-list-versions methylasso.wdl -f json | jq
{
  "software_versions": {
    "containers": {
      "quay.io/biocontainers/samtools": [
        "1.21--h96c455f_1"
      ],
      "ghcr.io/biowdl/docker-methylasso": [
        "main"
      ],
      "quay.io/biocontainers/bedtools": [
        "2.30.0--h7d7f7ad_2",
        "2.23.0--hdbcaa40_3",
        "2.31.1--hf5e1c6e_2"
      ]
    },
    "miniwdl": {
      "miniwdl": "v1.13.0",
      "miniwdl-slurm": "0.4.1.dev8+g54512d7"
    }
  }
}

Images

$ wdl-list-versions methylasso.wdl -f images
quay.io/biocontainers/samtools:1.21--h96c455f_1
ghcr.io/biowdl/docker-methylasso:main
quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2
quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3
quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2

License

EUPL-1.2