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The openBIS for Illumina NGS comes with predefined master data with the following schema:

To get the data into openBIS we have written drop boxes. Each drop box has a expected format how the data from the sequencer should be put in and will be later on processed and registered in openBIS.

Drop Boxes for openBIS Illumina NGS

create-flowcell-hiseq
Recommended Data Set Structure
110715_SN792_0054_BC035RACXX/
	runParameters.xml
	RunInfo.xml

Parses the two Illumina provided files 'runParameters.xml' and 'RunInfo.xml'
and creates one Sample of type 'ILLUMINA_FLOW_CELL' and sets Sample properties
from those two XML files. Additionally the number of lanes are read out and
are created as contained samples of type 'ILLUMINA_FLOW_LANE'.


read-rta-timestamp
Recommended Data Set Structure
110715_SN792_0054_BC035RACXX/
        RTAComplete.txt

Reads out the time stamp of the file 'RTAComplete.txt' and sets the
property for a finished sequencer called 'SEQUENCER_FINISHED' to the
time stamp of this file.


register-basecall-stats
Recommended Data Set Structure
C035RACXX_1/
	Basecall_Stats_C035RACXX/
	DemultiplexedBustardSummary.xml
	DemultiplexedBustardConfig.xml
	Makefile
	DemultiplexConfig.xml
	SampleSheet.mk
	support.txt

Registers an incoming directory as a 'BASECALL_STATS' data set in openBIS.
The name of the directory is used to search for the matching sample.

 

register-flowcell
Recommended Data Set Structure
130208_SN792_0204_BD1W0VACXX/
	Basecalling_Netcopy_complete_Read2.txt
	Basecalling_Netcopy_complete.txt
	Config/
	Data/
	First_Base_Report.htm
	ImageAnalysis_Netcopy_complete_Read1.txt
	ImageAnalysis_Netcopy_complete_Read2.txt
	ImageAnalysis_Netcopy_complete.txt
	InterOp/
	Logs/
	PeriodicSaveRates/
	Recipe/
	RTAComplete.txt
	RunInfo.xml
	runParameters.xml
	Thumbnail_Images/

Registers an incoming directory as a data set in openBIS. The name of the directory is used to
search for the matching sample.


register-lane-hiseq
Recommended Data Set Structure
Project_130208_SN792_0204_BD1W0VACXX_2/
	Sample_BSSE_QGF_LIBRARY_239_130208_SN792_0204_BD1W0VACXX_2/
		BSSE_QGF_LIBRARY_239_130208_SN792_0204_BD1W0VACXX_2_GCCAAT_L002_R1_001.fastq.gz
	Sample_BSSE_QGF_LIBRARY_240_130208_SN792_0204_BD1W0VACXX_2/
		BSSE_QGF_LIBRARY_240_130208_SN792_0204_BD1W0VACXX_2_CAGATC_L002_R1_001.fastq.gz
	Sample_BSSE_QGF_LIBRARY_241_130208_SN792_0204_BD1W0VACXX_2/
		BSSE_QGF_LIBRARY_241_130208_SN792_0204_BD1W0VACXX_2_ACTTGA_L002_R1_001.fastq.gz
		BSSE_QGF_LIBRARY_241_130208_SN792_0204_BD1W0VACXX_2_ACTTGA_L002_R1_002.fastq.gz
	Sample_BSSE_QGF_LIBRARY_304_130208_SN792_0204_BD1W0VACXX_2/
		BSSE_QGF_LIBRARY_304_130208_SN792_0204_BD1W0VACXX_2_ACAGTG_L002_R1_001.fastq.gz
	Sample_lane2/
		BSSE_QGF_POOL_243_D1W0VACXX_lane2_Undetermined_L002_R1_001.fastq.gz

Processes each flow lane of a Sequencing run and attaches the fastq files to
the correct corresponding library samples


register-runstatistics
Recommended Data Set Structure
130208_SN792_0204_BD1W0VACXX/
	Data/
		reports/
		Status_Files/
		Status.htm

Registers an incoming directory as a 'RUNINFO' data set in openBIS. The name of
the directory is used to search for the matching sample.


register-unaligned
130208_SN792_0204_BD1W0VACXX/
	Unaligned_1/
		Basecall_Stats_D1W0VACXX/
		DemultiplexConfig.xml
		DemultiplexedBustardConfig.xml
		DemultiplexedBustardSummary.xml
		Makefile
		nohup.out
		Project_130208_SN792_0204_BD1W0VACXX_1/
		SampleSheet.mk
		support.txt
		Temp
		Undetermined_indices
	Unaligned_2/
	Unaligned_3/
	Unaligned_4/
	Unaligned_5/
	Unaligned_6/
	Unaligned_7/
	Unaligned_8/

Splits up this complex data set into two different data sets and
moves the corresponding file into those drop boxes 

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