Usage on different compute systems

Accessing tool/workflow

Workflow consists of three modules:

1. Preqc module consists of bam to fasta conversion, k-mer analysis and genome profiling processes.
2. Assembly module consists of processing CCS data using IPA
3. Post assembly module consists of assembly evaluation and assessing completeness.

Dependencies

The following packages are used by the pipeline.

nextflow/21.04.3
samtools/1.12
jellyfish/2.3.0
genomescope/2.0
ipa/1.3.1
quast/5.0.2
busco/5.4.3
HiFiAdapterFilt/2.0.0

Pawsey

Running on Setonix at Pawsey

module load nextflow/23.04.1
module load singularity/3.8.6
nextflow run hifi_assembly.nf --bam_folder <PATH TO THE BAM FOLDER> --project_id director2172  -profile setonix

NCI

Facility access

One should have a user account set with NCI to access gadi high performance computational facility. Setting up a NCI account is mentioned in detail at the following URL: https://opus.nci.org.au/display/Help/Setting+up+your+NCI+Account

Documentation for a specific infrastructure should go into a infrastructure documentation template https://github.com/AustralianBioCommons/doc_guidelines/blob/master/infrastructure_optimisation.md

Running on GADI at NCI

Here is an example that can be used to run a phased assembly on Gadi utilising if89 (shared tools and workflow repository):

module load nextflow
module load singularity
nextflow run hifi_assembly.nf --bam_folder <PATH TO THE BAM FOLDER> --project_id xl04 --storage_paths gdata/if89+gdata/ll61 -profile if89

Running the workflow on GADI at NCI using if89 project

1. Login to Gadi with your credentials.
2. Join the if89 project, if you have not already. See this link for details on how to join.
3. Use the following script to run the workflow:

cd <hifi_genome_assembly_location>
hifi_assembly.nf --bam_folder <PATH_TO_BAM_FOLDER> -profile if89