Dx wrapper to run the bcl2fastq demultiplexing tool
This is the source code for an app that runs on the DNAnexus Platform.
Takes in the tar.gz packets of data uploaded from the NovaSeq machine as sequencing data was generated. OR the sentinel record file that was generated during dx-streaming-upload. Untars the files to reconstruct the NovaSeq output directory structure and demultiplexes the base call files to paired fastq.tar.gz for samples in the SampleSheet.csv based on the barcode sequences.
This app may be executed as a standalone app or as part of an analysis pipeline. Used as the first step when sequencing data is streamed from the sequencer to DNAnexus before bioinformatics analysis can begin.
The default instance (mem2_ssd1_v2_x32) has 32 cores, 125GB RAM and 1116GB of storage. For large flowcells it may be necessary to use a larger instance with more storage (such as mem3_ssd2_v2_x32).
This app requires
- SampleSheet.csv
- upload sentinel record
- array of tar.gz containing the output packets from the sequencer
Optional input parameters:
- advanced options for running bcl2fastq
- uploads all data from the sequencer (except for bcl files)
- including the demultiplexed fastq files in the folder where they are generated (Data/Intensities/BaseCalls)
- all files in
Logs/are uploaded to a single tar (Logs.tar.gz) - all files in
InterOp/are uploaded to a single tar (InterOp.tar.gz)
The applet depends on the bcl2fastq .deb file which is stored as an asset on DNAnexus.