run_on_nci.md

Run on NCI

• Run on NCI
  • Assumptions
  • 1. Modify nextflow_pipeface.config
  • 2. Start persistent session (optional)
  • 3. Get pipeline dependencies
  • 4. Run pipeface
  • Information

Assumptions

• Running pipeline on Australia's National Computational Infrastructure (NCI)
• Access to if89 project (to access software installs used by pipeface)
• Access to xy86 project (to access variant databases used by pipeface, only required if running variant annotation)

1. Modify nextflow_pipeface.config

Modify the NCI project to which to charge the analysis. Eg:

    project = 'kr68'

Modify access to project specific directories. Eg:

    storage = 'gdata/if89+gdata/xy86+scratch/kr68+gdata/kr68+gdata/ox63'

Note: Don't remove access to if89 gdata (gdata/if89) and xy86 gdata (gdata/xy86). These are required to access software installs and variant annotation databases used in the pipeline

2. Start persistent session (optional)

Pipeface can be run within a persistent session

3. Get pipeline dependencies

You may use the centrally installed nextflow environmental module available on NCI to access the nextflow dependency. Eg:

module load nextflow/24.04.5

4. Run pipeface

nextflow run pipeface.nf -params-file ./config/parameters_pipeface.json -config ./config/nextflow_pipeface.config

Information

Please keep in mind that some datasets will require modifications to the default resources (particularly memory, disk usage, walltime). For example WGS data with greater than typical (~30x) sequencing depth.