Routine IRIDA Upload

Pipeline for performing routine uploads of illumina sequence data to the IRIDA analysis platform.

Usage

nextflow run BCCDC-PHL/routine-irida-upload \
  --run_dir <illumina run directory> \
  --outdir <output directory> \
  [--config <irida uploader config>]

Outputs

<outdir>
├── <run_id>_irida_uploader.log
└── <run_id>_irida_uploader_status.info