spec.yml

# the build part will be used to create an image with `nfm build`
# required_env is the required entry and it specifies the environment needed to run the analyses,
# required_env will be also used as an additional environment during testing with `nfm test`
# entrypoint - an optional entrypoint for the container (niflow-{ORGANIZATION}-{WORKFLOW} is the default value)
build:
  # example below, see full Neurodocker spcification: https://github.com/ReproNim/neurodocker#supported-software
  required_env:
    base:
      image: debian:stretch
      pkg-manager: apt
    miniconda:
      conda_install: [python=3.7, nipype]
#    fsl:
#      version: 5.0.10
#    afni:
#      version: latest
#
# optional entrypoint, for python, the default value is
#  entrypoint: /opt/miniconda-latest/envs/testkraken/bin/niflow-{ORGANIZATION}-{WORKFLOW}

# test specification
test:
  # default location for data in the niflows is test/data in the workflow path
  data:
    type: workflow_path
    location: test/data
  # default location for scripts in the niflows is test/scripts in the workflow path
  scripts: test/scripts

  # additional (to the one defined in the build.required_env) environments for testing
  # a simple example that has only one base image and one miniconda environment
  env:
    base:
    - image: debian:stretch
      pkg-manager: apt
    miniconda:
    - conda_install: [python=3.5, nipype]

  # specification for the analysis that will be run and the needed input (input files expected to be in the data dir),
  # if script is provided, it should be in the scripts directory
  analysis:
    inputs: []
    command: niflow-{ORGANIZATION}-{WORKFLOW}
#  # specification for the output testing: script should be either in the scripts dir or from TestKraken
#  # file should be an output name and the reference one should be in the data dir
  tests: []
#  - file: out_name
#    name: regr1
#    script: test_obj_eq.py