brilator / arc

ARC - Annotated Research Context

ARCs

for details, see https://github.com/nfdi4plants/ARC-specification

ARC directory structure

/isa.investigation.xlsx : main investigation file (in XLSX format), contains top-level information about the investigation and links to studies and assays

/LICENSE : license file for the arc

/arc.cwl : (optional) executes all runs

Studies

All input material or (external) data resources are considered studies (immutable input data)

/assays/<yourStudyName> : folder for an essay, name is arbitrary

/assays/<yourStudyName>/resources : assay dataset

/assays/<yourStudyName>/protocols : assay protocol as text (e.g SOP)

/assays/<yourStudyName>/isa.study.xlsx : per-assay ISA file, contains only info about this assay (in XLSX format)

Assays

All measurement (self-generated) datasets are considered assays (immutable input data)

/assays/<yourAssayName> : folder for an essay, name is arbitrary

/assays/<yourAssayName>/dataset : assay dataset

/assays/<yourAssayName>/protocols : assay protocol as text (e.g SOP)

/assays/<yourAssayName>/isa.assay.xlsx : per-assay ISA file, contains only info about this assay (in XLSX format)

Workflows

All programmatic components of an ARC should go here, in the form of code and environment.

/workflows/<yourWorkflowName>/ : folder for code and its environment (workflow specifications), contains all files needed to specify a workflow. Also packages and other includes needed should go here.

/workflows/<yourWorkflowName>/Dockerfile : top-level Dockerfile [optional] in which all code/workflow should execute

/workflows/<yourWorkflowName>/[codefiles;...] : code files/scripts for computation

Runs

Runs are all artifacts that result by computation from studies, assays or other runs.

/runs/<yourRunResultName> : folder for results of your run aka. workflow execution

/runs/<yourRunResultName>/[files;...] : run result files (plots, tables, etc.)

/runs/<yourRunResultName>.cwl : executes a script or workflow and produces run results accordingly.