Docker step

Cloudgene supports the execution of commands inside a docker container.

Tip

All input and output parameters can be used inside the container since the workspace of a job is mounted automatically.

Parameters

Parameter Required Description
type yes Type has to be docker
image yes Docker image name inclusive version (e.g. library/ubuntu or biocontainers/vcftools)
cmd yes The command that should be executed
stdout no Use stdout as step's output (default: false)

Examples

VCFTools from biocontainers

The following example starts an image from biocontainers and executes vcftools to calculate allele frequencies:

name: Allele Frequencies from VCF
version: 1.0
workflow:
  steps:
    - name: Calculate frequencies
      type: docker
      image: biocontainers/vcftools
      cmd:  vcftools --gzvcf $vcf --freq --out $output
  inputs:
    - id: vcf
      description: VCF File
      type: local_file
  outputs:
    - id: output
      description: Frequencies
      type: local_file