Workflows

What is a Workflow?
15 Workflows visible to you, out of a total of 15
Work-in-progress

This is a Nextflow implementaion of the GATK Somatic Short Variant Calling workflow. This workflow can be used to discover somatic short variants (SNVs and indels) from tumour and matched normal BAM files following GATK's Best Practices Workflow. The workflowis currently optimised to run efficiently and at scale on the National Compute Infrastructure, Gadi.

GermlineStructuralV-nf is a pipeline for identifying structural variant events in human Illumina short read whole genome sequence data. GermlineStructuralV-nf identifies structural variant and copy number events from BAM files using Manta, Smoove, and TIDDIT. Variants are then merged using SURVIVOR, ...

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

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