Table 1.

Automatically generated pISA-tree directories and metadata files and recommended allocation of data files.

created directories/files	pISA-tree levels
	INVESTIGATION	STUDY	ASSAY
			wet-lab ASSAY	dry-lab ASSAY
level-specific metadata files	_INVESTIGATION_METADATA.TXT phenodata_yyyymmdd.txt (master sample table) featuredata_yyyymmdd.txt (variable description file)	_STUDY_METADATA.txt	_ASSAY_METADATA.TXT analytes.txt (analyte table)	_ASSAY_METADATA.TXT analytes.txt (analyte table)
input	—	—	—	input data set(s) or file(s) containing path(s) to input data
scripts	—	—	—	scripts, pipelines, workflows or commands used for the analyses
output	—	—	pre-processed results	final results
output/raw	—	—	raw result files, e.g. data collected from the machine	—
reports	summary reports for project partners and stakeholders	sample handling or any other study related protocols or reports	assay specific protocols, laboratory logs	documented procedures, protocols, log files with tool(s) version(s) used for the analyses
presentations	any presentation related to the project	—	—	—
other	—	—	other relevant files not included elsewhere	other relevant files not included elsewhere

Each level contains level-specific metadata files and directories containing data. ‘—’ directory not created at this level.