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

/isa.studies.xlsx : (optional) posibillity to group assays into studies within one investigation, contains mostly sample characteristics

/LICENSE : license file for the arc

/arc.cwl : (optional) executes all runs

All measurment (self generated) datasets are considert as assays (immutable input data)

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

/assays/<assay>/dataset : assay dataset

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

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

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

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

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

The place for external data (mapping files, gene info, etc.)

/externals/[e.g. mapman-ontology-301120.txt;...] : external reference / knowledge files, hard included

/externals/isa.tab : description of external reference / knowledge files, XLSX format

Runs are all artefacts that result by some computation from the assays.

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

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

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