/isa.investigation.xlsx
: main investigation file (in XLSX format), contains top-level information about the investigation and links to assays
/isa.studies.xlsx
: (optional) possibility 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 measurement (self generated) datasets are considered 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.