Containers

5 functions for running containerized tools. Supports Docker, Podman, Singularity, and OCI-based sandboxing via bubblewrap. Integrated with the BioContainers registry for 9,000+ bioinformatics tools.

container_run

Run a command inside a container image. Auto-detects the available runtime (Docker > Podman > Singularity > bwrap).

container_run(image, command, opts?) -> map

Parameter	Type	Description
image	string	OCI image reference
command	string \| list	Command to execute
opts.mounts	list	Volume mounts [{src, dst, mode}]
opts.env	map	Environment variables
opts.workdir	string	Working directory inside container

Returns: {"exit_code": int, "stdout": string, "stderr": string}

let result = container_run(
  "quay.io/biocontainers/samtools:1.19--h50ea8bc_0",
  "samtools view -c input.bam",
  {mounts: [{src: ".", dst: "/data", mode: "rw"}], workdir: "/data"}
)
println("Read count:", trim(result.stdout))

container_pull

Pull a container image to local cache.

container_pull(image) -> string

container_pull("quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0")
container_pull("quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0")

tool_search

Search the BioContainers registry for tools by name or keyword.

tool_search(query, opts?) -> list

let results = tool_search("samtools")
for tool in results {
  println(tool.name, "-", tool.description)
}

# Search with limit
tool_search("variant caller", {limit: 5})

tool_pull

Pull a BioContainers tool by name and optional version.

tool_pull(name, version?) -> string

tool_pull("samtools")                    # latest version
tool_pull("samtools", "1.19")            # specific version
tool_pull("bwa-mem2", "2.2.1")           # returns image path

tool_info

Get detailed information about a BioContainers tool, including available versions.

tool_info(name) -> map

let info = tool_info("gatk")
println(info.name, "-", info.description)
for v in info.versions {
  println(v.version, "-", v.image)
}
# 4.5.0.0 - quay.io/biocontainers/gatk4:4.5.0.0--py39...
# 4.4.0.0 - quay.io/biocontainers/gatk4:4.4.0.0--py39...