Workflows

What is a Workflow?
9 Workflows visible to you, out of a total of 9
Stable

Fastq-to-BAM @ NCI-Gadi is a genome alignment workflow that takes raw FASTQ files, aligns them to a reference genome and outputs analysis ready BAM files. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel, either massively parallel using the scatter-gather approach or parallel by sample. It consists of a number of stages and follows the BROAD Institute's best practice ...

Type: Shell Script

Creators: Cali Willet, Tracy Chew, Georgina Samaha, Rosemarie Sadsad, Andrey Bliznyuk, Ben Menadue, Rika Kobayashi, Matthew Downton, Yue Sun

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.146.1

Stable

RNASeq-DE @ NCI-Gadi processes RNA sequencing data (single, paired and/or multiplexed) for differential expression (raw FASTQ to counts). This pipeline consists of multiple stages and is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes to run each stage in parallel.

Infrastructure_deployment_metadata: Gadi (NCI)

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.152.1

Work-in-progress

Shotgun Metagenomics Analysis

Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more

Description

The input for this analysis is paired end next generation sequencing data from metagenomic samples. The workflow is designed to be modular, so that individual modules can be run depending on the nature of the metagenomics project at hand. More modules will be added as we develop them - this repo is a work in progress!

These scripts have been written ...

Type: Shell Script

Creators: Cali Willet, Rosemarie Sadsad, Tracy Chew, Smitha Sukumar, Elena Martinez, Christina Adler, Henry Lydecker, Fang Wang

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.327.1

Work-in-progress

Germline-ShortV @ NCI-Gadi is an implementation of the BROAD Institute's best practice workflow for germline short variant discovery. This implementation is optimised for the National Compute Infrastucture's Gadi HPC, utilising scatter-gather parallelism to enable use of multiple nodes with high CPU or memory efficiency. This workflow requires sample BAM files, which can be generated using the Fastq-to-bam @ NCI-Gadi pipeline. Germline-ShortV can be applied ...

Type: Shell Script

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

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.143.1

Work-in-progress

Somatic-ShortV @ NCI-Gadi is a variant calling pipeline that calls somatic short variants (SNPs and indels) from tumour and matched normal BAM files following GATK's Best Practice Workflow. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel. ...

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.148.1

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

Stable

Flashlite-Juicer is a PBS implementation of Juicer for University of Queensland's Flashlite HPC.

Infrastructure_deployment_metadata: FlashLite (QRISCloud)

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Nathaniel Butterworth

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.150.1

Work-in-progress

Bootstrapping-for-BQSR @ NCI-Gadi is a pipeline for bootstrapping a variant resource to enable GATK base quality score recalibration (BQSR) for non-model organisms that lack a publicly available variant resource. This implementation is optimised for the National Compute Infrastucture's Gadi HPC. Multiple rounds of bootstrapping can be performed. Users can use Fastq-to-bam @ NCI-Gadi and Germline-ShortV @ NCI-Gadi to ...

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.153.1

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

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