demux

Synopsis

singularity run [run options...] --app demux <container> [app options...]

Description

Demultiplex data. Generate per-sample FASTQ files from the raw sequence data consisting of BCL files.

Warning

The demultiplexing software bcl2fastq is not shipped with prebuilt versions of MIPTools. To demultiplex BCL files, you must download the software, place it in the programs directory, and build MIPtools from source.

Options

# Required
-s    Path to the sample sheet for demultiplexing.

# Optional
-h    Print the help page.

Sample Sheet

The sample sheet must be present in the directory mounted to /opt/analysis.

Examples

singularity run \
  -B base_resources:/opt/resources \
  -B bcl_dir:/opt/data \
  -B fastq_root_dir:/opt/analysis \
  --app demux miptools.sif -s SampleSheet.csv