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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/JaneliaSciComp/tethered-fly-pipeline/master/nextflow_schema.json",
"title": "Tethered fly pipeline parameters",
"description": "This pipeline uses Nextflow and processes videos of tethered flies using APT to produce tracking output.",
"type": "object",
"definitions": {
"data": {
"title": "Data",
"type": "object",
"description": "Filepaths to directories and files used for input and output",
"properties": {
"input_dir": {
"type": "string",
"description": "Top level directory for experiment containing all individual fly subdirectories",
"fa_icon": "fas fa-folder"
},
"output_dir": {
"type": "string",
"description": "Directory where final results `.trk`, `_3dres.mat` will be generated. The per fly and per video results will be generated in the corresponding subfolders as found in the input, e.g., `.../fly4315/C001H001S0002/C001H001S0002_c.trk`",
"fa_icon": "fas fa-folder"
},
"tmp_tracking_dir": {
"type": "string",
"description": "Directory containing the intermediate results generated during the `detect` step",
"fa_icon": "fas fa-folder"
},
"scratch_dir": {
"type": "string",
"description": "Temp scratch directory for holding results before moving them to final destination",
"fa_icon": "fas fa-folder"
},
"label_filename": {
"type": "string",
"description": "e.g. `/groups/branson/bransonlab/apt/experiments/data/sh_trn5017_20200121_stripped.lbl`",
"fa_icon": "fas fa-file"
},
"body_axis_lookup_filename": {
"type": "string",
"description": ".csv file containing fly numbers with the corresponding body axis .lbl files e.g. `/groups/huston/hustonlab/flp-chrimson_experiments/fly2BodyAxis_lookupTable_Ben.csv`",
"fa_icon": "fas fa-file"
},
"crop_regression_filename": {
"type": "string",
"description": "e.g. `/groups/branson/bransonlab/mayank/stephen_copy/crop_regression_params.mat`",
"fa_icon": "fas fa-file"
},
"model_name": {
"type": "string",
"description": "e.g. `stephen_20200124`",
"fa_icon": "fas fa-file"
},
"calibrations_filename": {
"type": "string",
"description": ".csv file containing fly numbers with the corresponding calibration files",
"fa_icon": "fas fa-file"
},
"model_cache_dirname": {
"type": "string",
"description": "`/groups/branson/bransonlab/mayank/stephen_copy/apt_cache`",
"fa_icon": "fas fa-file"
},
"flydata_dirname_pattern": {
"type": "string",
"description": "Regex pattern for selecting the fly directories. This can be used for running the pipeline only for one or two flies for example: `fly123[4,8]` - selects only `fly1234` and `fly1238` as inputs. Default: `fly[0-9]*`",
"fa_icon": "fas fa-star-of-life"
},
"flydata_maxdepth_search": {
"type": "integer",
"description": "If greater than 0 it specifies how many levels to look for flydata directories under input_dir. Default: `0` (unlimitted)",
"fa_icon": "fas fa-square"
},
"sideview_videoname_pattern": {
"type": "string",
"description": "Filename pattern for **SIDE** view videos. Changing this may require settting `frontview_videoname_pattern` so that we process the side and front view in pairs. Default: `C001*.avi`",
"fa_icon": "fas fa-star-of-life"
},
"frontview_videoname_pattern": {
"type": "string",
"description": "Filename pattern for **FRONT** view videos. Changing this may require settting `sideview_videoname_pattern` so that we process the side and front view in pairs. Default: `C002*.avi`",
"fa_icon": "fas fa-star-of-life"
},
"sideview_detect_result_suffix": {
"type": "string",
"description": "Filename suffix used for **SIDE** view intermediated results. Default: `_side`",
"fa_icon": "fas fa-file-word"
},
"frontview_detect_result_suffix": {
"type": "string",
"description": "Filename suffix used for **FRONT** view intermediate results. Default: `_front`",
"fa_icon": "fas fa-file-word"
}
},
"required": [
"i",
"o",
"tmp_tracking_dir",
"label_filename",
"body_axis_lookup_filename",
"crop_regression_filename",
"model_name",
"calibrations_filename",
"model_cache_dirname"
],
"fa_icon": "fas fa-database"
},
"detect_parameters": {
"title": "Detection parameters",
"type": "object",
"description": "Parameters for the detection step",
"properties": {
"sideview_crop_size": {
"type": "string",
"description": "Default crop size used for **SIDE** view. Only change this if you know how this impacts the algorithm. Default: `230,350`",
"hidden": true,
"fa_icon": "fas fa-crop-alt"
},
"frontview_crop_size": {
"type": "string",
"description": "Default crop size used for **FRONT** view. Only change this if you know how this impacts the algorithm. Default: `350,350`",
"hidden": true,
"fa_icon": "fas fa-crop-alt"
},
"apt_detect_cpus": {
"type": "string",
"fa_icon": "fas fa-microchip",
"description": "Number of CPU cores for detection. Default: 2"
},
"apt_detect_memory": {
"type": "string",
"fa_icon": "fas fa-memory",
"description": "Amount of memory for detection. Default: 30 G"
}
},
"fa_icon": "fas fa-bullseye"
},
"track_parameters": {
"title": "Tracking parameters",
"type": "object",
"description": "Parameters for the tracking step",
"properties": {
"apt_track_cpus": {
"type": "string",
"fa_icon": "fas fa-microchip",
"description": "Number of CPU cores for tracking. Default: 3"
},
"apt_track_memory": {
"type": "string",
"fa_icon": "fas fa-memory",
"description": "Amount of memory for tracking. Default: 45 G"
}
},
"fa_icon": "fas fa-bullseye"
},
"containers": {
"title": "Container Options",
"type": "object",
"fa_icon": "fab fa-docker",
"properties": {
"apt_detect_container": {
"type": "string",
"description": "Docker container for running detect using APT. Default: `registry.int.janelia.org/huston/apt_detect:1.0`",
"fa_icon": "fas fa-box-open",
"hidden": true
},
"apt_track_container": {
"type": "string",
"description": "Docker container for running tracking using APT. Default: `registry.int.janelia.org/huston/apt_track:1.0`",
"fa_icon": "fas fa-box-open",
"hidden": true
}
},
"description": "Customize the Docker containers used for each pipeline step"
},
"other": {
"title": "Other Options",
"type": "object",
"fa_icon": "fas fa-list-ul",
"properties": {
"singularity_cache_dir": {
"type": "string",
"description": "Shared directory where Singularity containers are cached. Default: $shared_work_dir/singularity_cache or $HOME/.singularity_cache",
"fa_icon": "fas fa-folder-open",
"hidden": true
},
"singularity_user": {
"type": "string",
"fa_icon": "fas fa-user",
"description": "User to use for running Singularity containers. Default: $USER",
"hidden": true,
"help_text": "This is automatically set to `ec2-user` when using the 'tower' profile"
},
"runtime_opts": {
"type": "string",
"fa_icon": "fas fa-terminal",
"help_text": "Runtime options for Singularity must include mounts for any directory paths you are using. You can also pass the --nv flag here to make use of NVIDIA GPU resources. For example, `--nv -B /your/data/dir -B /your/output/dir`\n",
"description": "Runtime options for the container engine being used (e.g. Singularity or Docker)."
},
"lsf_opts": {
"type": "string",
"description": "Options for LSF cluster at Janelia, when using the lsf profile.",
"fa_icon": "fas fa-terminal"
}
},
"description": "Other global options affecting all pipelines stages"
}
},
"allOf": [
{
"$ref": "#/definitions/data"
},
{
"$ref": "#/definitions/detect_parameters"
}
]
}