ARCs

ARC directory structure

/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

Assay

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)

workflows (aka. codespace, code, code capsules, codecaps)

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

Externals

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 (aka. computations)

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.