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[ENH] Add descriptors and sample invocations for BIDScoin (nipoppy#267)
* add descriptors and sample invocations for BIDSCOIN * rename descriptors * expand on descriptions in Boutiques descriptors * update BIDScoin config/descriptor to not use container (difficult because of GUI components) * fix test
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nipoppy_cli/nipoppy/data/descriptors/bidscoiner-4.3.2.json
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| { | ||
| "name": "bidscoiner", | ||
| "description": "bidscoiner (part of BIDScoin) to run BIDS conversion based on a YAML configuration file (bidsmap). See https://bidscoin.readthedocs.io/en/latest/workflow.html#step-2-running-the-bidscoiner", | ||
| "tool-version": "4.3.2+qt5", | ||
| "schema-version": "0.5", | ||
| "command-line": "bidscoiner [SOURCEFOLDER] [BIDSFOLDER] [PARTICIPANT_LABEL] [BIDSMAP] [FORCE] [CLUSTER] [NATIVESPEC]", | ||
| "inputs": [ | ||
| { | ||
| "name": "sourcefolder", | ||
| "id": "sourcefolder", | ||
| "description": "The study root folder containing the raw source data", | ||
| "type": "String", | ||
| "optional": false, | ||
| "value-key": "[SOURCEFOLDER]" | ||
| }, | ||
| { | ||
| "name": "bidsfolder", | ||
| "id": "bidsfolder", | ||
| "description": "The destination / output folder with the bids data", | ||
| "type": "String", | ||
| "optional": false, | ||
| "value-key": "[BIDSFOLDER]" | ||
| }, | ||
| { | ||
| "name": "participant_label", | ||
| "id": "participant_label", | ||
| "description": "Space separated list of selected sub-# names / folders to be processed (the sub-prefix can be removed). Otherwise all subjects in the sourcefolder will be selected", | ||
| "type": "String", | ||
| "list": true, | ||
| "optional": true, | ||
| "command-line-flag": "-p", | ||
| "value-key": "[PARTICIPANT_LABEL]" | ||
| }, | ||
| { | ||
| "name": "bidsmap", | ||
| "id": "bidsmap", | ||
| "description": "The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the basename (i.e. no \"/\" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml", | ||
| "type": "String", | ||
| "optional": true, | ||
| "default-value": "bidsmap.yaml", | ||
| "command-line-flag": "-b", | ||
| "value-key": "[BIDSMAP]" | ||
| }, | ||
| { | ||
| "name": "force", | ||
| "id": "force", | ||
| "description": "Process all subjects, regardless of existing subject folders in the bidsfolder. Otherwise these subject folders will be skipped", | ||
| "type": "Flag", | ||
| "optional": true, | ||
| "command-line-flag": "-f", | ||
| "value-key": "[FORCE]" | ||
| }, | ||
| { | ||
| "name": "cluster", | ||
| "id": "cluster", | ||
| "description": "Use the DRMAA library to submit the bidscoiner jobs to a high-performance compute (HPC) cluster", | ||
| "type": "Flag", | ||
| "optional": true, | ||
| "command-line-flag": "-c", | ||
| "value-key": "[CLUSTER]" | ||
| }, | ||
| { | ||
| "name": "nativespec", | ||
| "id": "nativespec", | ||
| "description": "Opaque DRMAA argument with native specifications for submitting bidscoiner jobs to the HPC cluster. NB: Use quotes and include at least one space character to prevent premature parsing (default: -l walltime=00:30:00,mem=4gb)", | ||
| "type": "String", | ||
| "optional": true, | ||
| "default-value": "-l walltime=00:30:00,mem=4gb", | ||
| "command-line-flag": "-n", | ||
| "value-key": "[NATIVESPEC]" | ||
| } | ||
| ], | ||
| "tags": {}, | ||
| "suggested-resources": { | ||
| "cpu-cores": 1, | ||
| "ram": 1, | ||
| "walltime-estimate": 60 | ||
| } | ||
| } |
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nipoppy_cli/nipoppy/data/descriptors/bidseditor-4.3.2.json
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| { | ||
| "name": "bidseditor", | ||
| "description": "bidseditor (part of BIDScoin) to edit an existing YAML configuration file (bidsmap). See https://bidscoin.readthedocs.io/en/latest/workflow.html#step-1b-running-the-bidseditor", | ||
| "tool-version": "4.3.2+qt5", | ||
| "schema-version": "0.5", | ||
| "command-line": "bidseditor [BIDSFOLDER] [BIDSMAP] [TEMPLATE]", | ||
| "inputs": [ | ||
| { | ||
| "name": "bidsfolder", | ||
| "id": "bidsfolder", | ||
| "description": "The destination folder with the (future) bids data", | ||
| "type": "String", | ||
| "optional": false, | ||
| "value-key": "[BIDSFOLDER]" | ||
| }, | ||
| { | ||
| "name": "bidsmap", | ||
| "id": "bidsmap", | ||
| "description": "The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the basename (i.e. no \"/\" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml", | ||
| "type": "String", | ||
| "optional": true, | ||
| "default-value": "bidsmap.yaml", | ||
| "command-line-flag": "-b", | ||
| "value-key": "[BIDSMAP]" | ||
| }, | ||
| { | ||
| "name": "template", | ||
| "id": "template", | ||
| "description": "The template bidsmap file with the default heuristics (this could be provided by your institute). If the bidsmap filename is just the basename (i.e. no \"/\" in the name) then it is assumed to be located in the bidscoin config folder. Default: bidsmap_dccn", | ||
| "type": "String", | ||
| "optional": true, | ||
| "command-line-flag": "-t", | ||
| "value-key": "[TEMPLATE]" | ||
| } | ||
| ], | ||
| "tags": {}, | ||
| "suggested-resources": { | ||
| "cpu-cores": 1, | ||
| "ram": 1, | ||
| "walltime-estimate": 60 | ||
| } | ||
| } |
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nipoppy_cli/nipoppy/data/descriptors/bidsmapper-4.3.2.json
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| { | ||
| "name": "bidsmapper", | ||
| "description": "bidsmapper (part of BIDScoin) to create/edit a YAML configuration file (bidsmap). See https://bidscoin.readthedocs.io/en/latest/workflow.html#step-1a-running-the-bidsmapper", | ||
| "tool-version": "4.3.2+qt5", | ||
| "schema-version": "0.5", | ||
| "command-line": "bidsmapper [SOURCEFOLDER] [BIDSFOLDER] [BIDSMAP] [TEMPLATE] [PLUGINS] [SUBPREFIX] [SESPREFIX] [UNZIP] [STORE] [AUTOMATED] [FORCE] [NO_UPDATE]", | ||
| "inputs": [ | ||
| { | ||
| "name": "sourcefolder", | ||
| "id": "sourcefolder", | ||
| "description": "The study root folder containing the raw source data folders", | ||
| "type": "String", | ||
| "optional": false, | ||
| "value-key": "[SOURCEFOLDER]" | ||
| }, | ||
| { | ||
| "name": "bidsfolder", | ||
| "id": "bidsfolder", | ||
| "description": "The destination folder with the (future) bids data and the bidsfolder/code/bidscoin/bidsmap.yaml output file", | ||
| "type": "String", | ||
| "optional": false, | ||
| "value-key": "[BIDSFOLDER]" | ||
| }, | ||
| { | ||
| "name": "bidsmap", | ||
| "id": "bidsmap", | ||
| "description": "The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the basename (i.e. no '/' in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml", | ||
| "type": "String", | ||
| "optional": true, | ||
| "default-value": "bidsmap.yaml", | ||
| "command-line-flag": "-b", | ||
| "value-key": "[BIDSMAP]" | ||
| }, | ||
| { | ||
| "name": "template", | ||
| "id": "template", | ||
| "description": "The bidsmap template file with the default heuristics (this could be provided by your institute). If the bidsmap filename is just the basename (i.e. no '/' in the name) then it is assumed to be located in the bidscoin config folder. Default: bidsmap_dccn", | ||
| "type": "String", | ||
| "optional": true, | ||
| "command-line-flag": "-t", | ||
| "value-key": "[TEMPLATE]" | ||
| }, | ||
| { | ||
| "name": "plugins", | ||
| "id": "plugins", | ||
| "description": "List of plugins to be used. Default: the plugin list of the study/template bidsmap)", | ||
| "type": "String", | ||
| "list": true, | ||
| "optional": true, | ||
| "command-line-flag": "-p", | ||
| "value-key": "[PLUGINS]" | ||
| }, | ||
| { | ||
| "name": "subprefix", | ||
| "id": "subprefix", | ||
| "description": "The prefix common for all the source subject-folders (e.g. 'Pt' is the subprefix if subject folders are named 'Pt018', 'Pt019', ...). Use '*' when your subject folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'sub-'", | ||
| "type": "String", | ||
| "optional": true, | ||
| "command-line-flag": "-n", | ||
| "value-key": "[SUBPREFIX]" | ||
| }, | ||
| { | ||
| "name": "sesprefix", | ||
| "id": "sesprefix", | ||
| "description": "The prefix common for all the source session-folders (e.g. 'M_' is the subprefix if session folders are named 'M_pre', 'M_post', ..). Use '*' when your session folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'ses-'", | ||
| "type": "String", | ||
| "optional": true, | ||
| "command-line-flag": "-m", | ||
| "value-key": "[SESPREFIX]" | ||
| }, | ||
| { | ||
| "name": "unzip", | ||
| "id": "unzip", | ||
| "description": "Wildcard pattern to unpack tarball/zip-files in the sub/ses sourcefolder that need to be unzipped (in a tempdir) to make the data readable. Default: the value of the study/template bidsmap", | ||
| "type": "String", | ||
| "optional": true, | ||
| "command-line-flag": "-u", | ||
| "value-key": "[UNZIP]" | ||
| }, | ||
| { | ||
| "name": "store", | ||
| "id": "store", | ||
| "description": "Store provenance data samples in the bidsfolder/code/provenance folder (useful for inspecting e.g. zipped or transferred datasets)", | ||
| "type": "Flag", | ||
| "optional": true, | ||
| "command-line-flag": "-s", | ||
| "value-key": "[STORE]" | ||
| }, | ||
| { | ||
| "name": "automated", | ||
| "id": "automated", | ||
| "description": "Save the automatically generated bidsmap to disk and without interactively tweaking it with the bidseditor", | ||
| "type": "Flag", | ||
| "optional": true, | ||
| "command-line-flag": "-a", | ||
| "value-key": "[AUTOMATED]" | ||
| }, | ||
| { | ||
| "name": "force", | ||
| "id": "force", | ||
| "description": "Discard the previously saved bidsmap and logfile", | ||
| "type": "Flag", | ||
| "optional": true, | ||
| "command-line-flag": "-f", | ||
| "value-key": "[FORCE]" | ||
| }, | ||
| { | ||
| "name": "no_update", | ||
| "id": "no_update", | ||
| "description": "Do not update any sub/sesprefixes in or prepend the sourcefolder name to the <<filepath:regex>> expression that extracts the subject/session labels. This is normally done to make the extraction more robust, but could cause problems for certain use cases", | ||
| "type": "Flag", | ||
| "optional": true, | ||
| "command-line-flag": "--no-update", | ||
| "value-key": "[NO_UPDATE]" | ||
| } | ||
| ], | ||
| "tags": {}, | ||
| "suggested-resources": { | ||
| "cpu-cores": 1, | ||
| "ram": 1, | ||
| "walltime-estimate": 60 | ||
| } | ||
| } |
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7 changes: 7 additions & 0 deletions
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nipoppy_cli/nipoppy/data/examples/sample_invocations/bidscoin-4.3.2-convert.json
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| { | ||
| "sourcefolder": "[[NIPOPPY_DPATH_SOURCEDATA]]", | ||
| "bidsfolder": "[[NIPOPPY_DPATH_BIDS]]", | ||
| "participant_label": [ | ||
| "[[NIPOPPY_PARTICIPANT_ID]]" | ||
| ] | ||
| } |
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nipoppy_cli/nipoppy/data/examples/sample_invocations/bidscoin-4.3.2-edit.json
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| { | ||
| "bidsfolder": "[[NIPOPPY_DPATH_BIDS]]" | ||
| } |
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nipoppy_cli/nipoppy/data/examples/sample_invocations/bidscoin-4.3.2-prepare.json
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| { | ||
| "sourcefolder": "[[NIPOPPY_DPATH_SOURCEDATA]]", | ||
| "bidsfolder": "[[NIPOPPY_DPATH_BIDS]]" | ||
| } |
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