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README.md

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DEMUX_BCL2FQ

  • Wrapping Illumina's bcl2fastq (version 2.20.0.422) execution commands with user supplied values.
  • bcl2fastq's thread management is currently set to 10 read/write threads and a calculated value for processing threads
    • Currently (nproc -5)
  • A submission script is used to format for submission to an HPC cluster
    • All resources will be reserved for the submission.
    • An email will be sent to the notifications alias when submission occurs and once the qsub process completes
  • Execution must occur on one of the HPC submit nodes

Command Line Arguments

  • The submitter script currently accepts 2 command line arguments in the following order
    • The run folder name (e.g., 190114_A00527_0033_BH3WNYDRXX)
    • The full qualified linux format path to the sample sheet including the file name
      • /mnt/path/to/a/samplesheet.csv
    • The qsub command makes use of a flag (-l excl=true) that allows this submission to reserve all resources for a node of a queue -Currently when this job is viewed with a qstat command, the node will appear to have slots available though no other job will be allowed access.

Example Execution Commands

/mnt/research/tools/LINUX/DEMUX_BCL2FQ/SUBMITTER.BCL2FQ.sh /PATH/TO/RUN_FOLDER_NAME /PATH/TO/SampleSheetName.csv | bash

/mnt/research/tools/LINUX/DEMUX_BCL2FQ/SUBMITTER.BCL2FQ.sh /mnt/instrument_files/novaseq/190229_A0000_0001_AHPVJDDDXX/ /mnt/instrument_files/novaseq/190229_A0000_0001_AHPVJDDDXX/SampleSheetName.csv | bash

  • Note the pipe to bash at the end of the command for execute the qsub command generated by the submitter script