Workflows

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738 Workflows visible to you, out of a total of 793
Flashlite-Trinity
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

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Flashlite-Juicer
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

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Bootstrapping-for-BQSR @ NCI-Gadi
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

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Trinity @ NCI-Gadi
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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microPIPE: a pipeline for high-quality bacterial genome construction using ONT and Illumina sequencing
Stable

microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.

To build microPIPE we evaluated the performance of several tools at each step of bacterial genome assembly, including basecalling, assembly, and polishing. Results at each step were validated using the high-quality ST131 Escherichia coli strain EC958 (GenBank: HG941718.1). After appraisal of each step, we selected the best combination of ...

Type: Nextflow

Creators: Valentine Murigneux, Leah W Roberts,  Brian M Forde, Minh-Duy Phan, Nguyen Thi Khanh Nhu, Adam D Irwin, Patrick N A Harris, David L Paterson, Mark A Schembri, David M Whiley, Scott A Beatson 

Submitter: Valentine Murigneux

DOI: 10.48546/workflowhub.workflow.140.1

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GATK4 Fastq to joint-called cohort VCF with Cromwell on SLURM
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: Workflow Description Language

Creators: None

Submitter: Sarah Beecroft

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GATK4 Fastq to joint-called cohort VCF with Cromwell on local cluster (no job scheduler)
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: Workflow Description Language

Creators: None

Submitter: Sarah Beecroft

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16S_biodiversity_BIOM
Stable

This is a Galaxy workflow that uses to convert the16S BIOM file to table and figures. It is part of the metaDEGalaxy workflow MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data.

Type: Galaxy

Creator: Mike Thang

Submitter: Mike Thang

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HI-FRIENDS HI data cube source finding and characterization
Stable

This repository contains the workflow used to find and characterize the HI sources in the data cube of the SKA Data Challenge 2. It was developed to process a simulated SKA data cube data cube, but can be adapted for clean HI data cubes from other radio observatories.

The workflow is managed and executed using snakemake workflow management system. It uses https://spectral-cube.readthedocs.io/en/latest/ based on ...

Type: Snakemake

Creators: None

Submitter: Javier Moldon

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ORSON: workflow for prOteome and tRanScriptome functiOnal aNnotation
Stable

ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.

Type: Nextflow

Creators: Cyril Noel, Alexandre Cormier, Patrick Durand, Laura Leroi, Pierre Cuzin

Submitter: Patrick Durand

DOI: 10.48546/workflowhub.workflow.136.1

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