This repository contains structured documentation for microPIPE, including links to existing repositories and community resources, as well as a description of the optimisations achieved on the following compute systems:
- Pawsey Supercomputing Centre (Perth, Western Australia)
When using microPIPE to run the Oxford Nanopore data basecalling and demultiplexing, it is recommended to use the GPU resources. As a result, the basecalling step will be performed using the high accuracy model (instead of the fast model) and the workflow will complete faster than with only the CPU resources.
- The table below summarised the basecalling run time depending on the resources used.
| Resources (Cluster) | Basecalling model | Guppy Configuration file | Run time |
|---|---|---|---|
| GPU (Topaz) | high-accuracy | dna_r9.4.1_450bps_hac.cfg | 10h 17m 17s |
| CPU (Zeus) | fast | dna_r9.4.1_450bps_fast.cfg | 3d 19h 21m 31s |
To use GPU resources for basecalling and demultiplexing, use the --gpu flag in the main nextflow command:
nextflow main.nf --gpu true --basecalling --demultiplexing --samplesheet /path/to/samples.csv --fast5 /path/to/fast5/directory/ --datadir /path/to/datadir/ --outdir /path/to/outdir/
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You can make use of this template repository as a base template for a new GitHub repository.
General information about the guidelines
- This **template** repository contains a set of guidelines for documenting bioinformatics tools and workflows.
- The initial version uploaded to GitHub was informed by current documentation practices and structures used in the GitHub community.
- These guidelines will be further developed as needed to meet the requirements of the Australian BioCommons community.