invalid-example.json

{
    "cabinet": {
        "container_type": "singularity",
        "stages": ["bibsnet", "solve_world_hunger", "nibabies"],
        "verbose": true,
        "handle_missing_host_paths": "make_directories"
    },

    "stages": {
        "bibsnet": {
            "container_filepath": "/home/faird/shared/code/internal/pipelines/cabinet_container/cabinet_v2.4.3.sif",
            "container_args": {
                "--cleanenv": true,
                "--nv": true
            },
            "binds": [
                {
                    "host_path":"/home/faird/shared/data/BCP-MVP_BIBSNet/input/",
                    "container_path":"/input"
                },
                {
                    "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/derivatives/"
                },
                {
                    "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/work/",
                    "container_path":"/work"
                }
            ],
            "positional_args": [
                "/input", "/output", "participant"
            ],
            "flags": {
                "--parameter-json":"/home/cabinet/parameter-file-container.json",
                "-start":"prebibsnet",
                "-end":"postbibsnet",
                "-v": true,
                "--participant-label":"470437",
                "-w":"/work"
            }
        },
        "nibabies": {  
            "container_filepath": "/home/faird/shared/code/external/pipelines/nibabies/nibabies_t1-t2-derivatives_08102023.sif",
            "container_args": {
                "--cleanenv": true
            },
            "binds": [
                {
                    "host_path":"/home/faird/shared/data/BCP-MVP_BIBSNet/input/",
                    "container_path":"/bids_dir"
                },
                {
                    "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/derivatives/nibabies/",
                    "container_path":"/output_dir"
                },
                {
                    "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/work/",
                    "container_path":"/work"
                },
                {
                    "host_path":"/home/faird/shared/code/external/utilities/freesurfer_license/license.txt",
                    "container_path":"/opt/freesurfer/license.txt"
                },
                {
                    "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/derivatives/bibsnet/",
                    "container_path":"/derivatives"
                },
                {
                    "host_path":"/home/faird/tikal004/fake/file/path/",
                    "container_path":"/fake_path"
                }
            ],
            "positional_args": [
                "/bids_dir", "/output_dir", "participant"
            ],
            "flags": {
                "--project-goodvoxels": true,
                "--surface-recon-method": "mcribs",
                "--omp-nthreads": 3,
                "--resource-monitor": true,
                "--cifti-output": "91k",
                "-vv": true,
                "-w": "/work", 
                "--fd-radius": 35,
                "--derivatives": "/derivatives",
                "--age-months": 1,
                "--participant-label":"470437"
            }
        },
        "xcpd": {
            "container_args": {
                "--cleanenv": true
            },
            "binds": [
                {
                    "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/work/",
                    "container_path":"/work"
                },
                {
                    "host_path":"/home/faird/shared/code/external/utilities/freesurfer_license/license.txt",
                    "container_path":"/opt/freesurfer/license.txt"
                },
                {
                    "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/derivatives/",
                    "container_path":"/output_dir"
                },
                {
                    "host_path":"/home/faird/shared/code/external/pipelines/xcp_d_test_binds/20230712_fix-collection/xcp_d/xcp_d",
                    "container_path":"/usr/local/miniconda/lib/python3.8/site-packages/xcp_d"
                }
            ],
            "positional_args": [
                "/output_dir/nibabies", "/output_dir/", "participant"
            ],
            "flags": {
                "--input-type": "nibabies",
                "--cifti": true,
                "--despike":true,
                "--resource-monitor": true,
                "--dcan-qc": true,
                "-w": "/work",
                "--omp-nthreads": 3,
                "--warp-surfaces-native2std": true,
                "-f": 0.3,
                "-m": true,
                "-vv": true,
                "--participant-label": "470437" 
            }
        },
        "lolcow": {
            "container_filepath": "/home/faird/tikal004/lolcow.sif",
            "action": "exe",
            "positional_args": [
                "cowsay", "\"Thank you for testing CABINET\""
            ]
        }
    }
}