Workflows

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20 Workflows visible to you, out of a total of 20
Work-in-progress

The Flashlite-Supernova pipeline runs Supernova to generate phased whole-genome de novo assemblies from a Chromium prepared library on University of Queensland's HPC, Flashlite.

Infrastructure_deployment_metadata: FlashLite (QRISCloud)

Type: Shell Script

Creators: None

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.151.1

Stable

Flashlite-Trinity contains two workflows that run Trinity on the University of Queensland's HPC, Flashlite. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. Users can run Flashlite-Trinity on single samples, or smaller samples requiring <500Gb ...

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Georgina Samaha, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.149.1

Work-in-progress

Description: Trinity @ NCI-Gadi contains a staged Trinity workflow that can be run on the National Computational Infrastructure’s (NCI) Gadi supercomputer. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. ...

Type: Shell Script

Creators: Georgina Samaha, Rosemarie Sadsad, Tracy Chew, Matthew Downton, Andrey Bliznyuk, Rika Kobayashi, Ben Menadue, Ben Evans

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.145.1

Work-in-progress

SLURM HPC Cromwell implementation of GATK4 germline variant calling pipeline

See the GATK website for more information on this toolset

Assumptions

  • Using hg38 human reference genome build
  • Running using HPC/SLURM scheduling. This repo was specifically tested on Pawsey Zeus machine, primarily running in the /scratch partition.
  • Starting from short-read Illumina paired-end fastq files as input

Dependencies

The following versions have been ...

Type: Unrecognized workflow type

Creators: None

Submitter: Sarah Beecroft

Work-in-progress

Local Cromwell implementation of GATK4 germline variant calling pipeline

See the GATK website for more information on this toolset

Assumptions

  • Using hg38 human reference genome build
  • Running 'locally' i.e. not using HPC/SLURM scheduling, or containers. This repo was specifically tested on Pawsey Nimbus 16 CPU, 64GB RAM virtual machine, primarily running in the /data volume storage partition.
  • Starting from short-read Illumina paired-end fastq ...

Type: Unrecognized workflow type

Creators: None

Submitter: Sarah Beecroft

Stable

A porting of the Trinity RNA assembly pipeline, https://trinityrnaseq.github.io, that uses Nextflow to handle the underlying sub-tasks. This enables additional capabilities to better use HPC resources, such as packing of tasks to fill up nodes and use of node-local disks to improve I/O. By design, the pipeline separates the workflow logic (main file) and the cluster-specific configuration (config files), improving portability.

Based on a pipeline by Sydney Informatics Hub: ...

Type: Nextflow

Creator: Marco De La Pierre

Submitter: Marco De La Pierre

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