Workflows

What is a Workflow?

745 Workflows visible to you, out of a total of 794

entryTitleTest

UX trial team

Cryo-EM processing workflow

Type: Common Workflow Language

Creators: None

Submitter: Irene Sánchez

DOI: 10.48546/workflowhub.workflow.188.1

Download

Created: 15th Sep 2021 at 16:26

testEntryTitleNew

UX trial team

Cryo-EM processing workflow

Type: Common Workflow Language

Creators: None

Submitter: Irene Sánchez

DOI: 10.48546/workflowhub.workflow.183.1

Download

Created: 15th Sep 2021 at 14:56

Cryo electron microscopy of SARS-CoV-2 spike in prefusion state

UX trial team

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures

Type: Common Workflow Language

Creators: None

Submitter: Irene Sánchez

DOI: 10.48546/workflowhub.workflow.160.1

Download

Created: 14th Sep 2021 at 14:52, Last updated: 15th Sep 2021 at 14:14

SAMBA: Standardized and Automated MetaBarcoding Analyses workflow

SeBiMER

(Show All)

Stable

SAMBA is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to conduct reproducible eDNA analyses using Nextflow. SAMBA starts processing by verifying integrity of raw reads and metadata. Then all bioinformatics processing is done using commonly used procedure (QIIME 2 and DADA2) but adds new steps relying on dbOTU3 and microDecon to build high quality ASV count tables. Extended statistical analyses are also performed. Finally, SAMBA ...

Type: Nextflow

Creators: Cyril Noel, Alexandre Cormier, Laura Leroi, Patrick Durand, Laure Quintric

Submitter: Cyril Noel

DOI: 10.48546/workflowhub.workflow.156.1

Download

Created: 10th Sep 2021 at 14:40, Last updated: 10th Sep 2021 at 14:43

Germline-ShortV @ NCI-Gadi

Australian BioCommons, Sydney Informatics Hub

(Show All)

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

Download

Created: 17th Aug 2021 at 05:35, Last updated: 9th Sep 2021 at 02:34

Somatic-ShortV @ NCI-Gadi

Sydney Informatics Hub

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

Download

Created: 18th Aug 2021 at 00:14, Last updated: 9th Sep 2021 at 02:33

Flashlite-Supernova

Australian BioCommons, Sydney Informatics Hub

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

Download

Created: 18th Aug 2021 at 00:21, Last updated: 9th Sep 2021 at 02:31

Flashlite-Trinity

Australian BioCommons, Sydney Informatics Hub

(Show All)

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

Download

Created: 18th Aug 2021 at 00:17, Last updated: 7th Sep 2021 at 07:27

Flashlite-Juicer

Sydney Informatics Hub

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

Download

Created: 18th Aug 2021 at 00:19, Last updated: 7th Sep 2021 at 07:26

Bootstrapping-for-BQSR @ NCI-Gadi

Sydney Informatics Hub

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

Download

Created: 18th Aug 2021 at 00:26, Last updated: 7th Sep 2021 at 07:24

Workflows

Filters ×

Filters