Workflows

What is a Workflow?
76 Workflows visible to you, out of a total of 76

qcif/taxapus is a modular, reproducible Nextflow workflow for the conservative taxonomy assignment to DNA sequences, designed for high-confidence, auditable results in biosecurity and biodiversity contexts. The workflow integrates multiple bioinformatics tools and databases, automates best-practice analysis steps, and produces detailed reports with supporting evidence for each taxonomic assignment.

Workflow Overview

The pipeline orchestrates a series of analytical steps, each encapsulated ...

Type: Nextflow

Creators: Magdalena Antczak, Cameron Hyde, Lanxi (Daisy) Li, Valentine Murigneux, Sarah Williams, Michael Thang, Bradley Pease, Shaun Bochow, Grace Sun

Submitter: Magdalena Antczak

DOI: 10.48546/workflowhub.workflow.1782.1

Stable

A rapid and portable workflow for pond-side sequencing of bacterial pathogens for sustainable aquaculture using ONT long-read sequencing.

Stable

ONTViSc (ONT-based Viral Screening for Biosecurity)

Introduction

eresearchqut/ontvisc is a Nextflow-based bioinformatics pipeline designed to help diagnostics of viruses and viroid pathogens for biosecurity. It takes fastq files generated from either amplicon or whole-genome sequencing using Oxford Nanopore Technologies as input.

The pipeline can either: 1) perform a direct search on the sequenced reads, 2) generate clusters, 3) assemble the reads to generate longer contigs or 4) directly ...

Type: Nextflow

Creators: Marie-Emilie Gauthier, Craig Windell, Magdalena Antczak, Roberto Barrero

Submitter: Magdalena Antczak

DOI: 10.48546/workflowhub.workflow.683.3

Work-in-progress

The aim of this workflow is to handle the routine part of shotgun metagenomics data processing. The workflow is using the tools Kraken2 and Bracken for taxonomy classification and the KrakenTools to evaluate diversity metrics. This workflow was tested on Galaxy Australia. A How-to guide for the workflow can be found at: https://github.com/vmurigneu/kraken_howto_ga_workflows/blob/main/pages/taxonomy_kraken2_wf_guide.md

Stable

Nextflow Pipeline for DeepVariant

This repository contains a Nextflow pipeline for Google’s DeepVariant, optimised for execution on NCI Gadi.

Quickstart Guide

  1. Edit the pipeline_params.yml file to include:
  • samples: a list of samples, where each sample includes the sample name, BAM file path (ensure corresponding .bai is in the same directory), path to an optional regions-of-interest BED file (set to '' if not required), and the model type.
  • ref: path to the reference FASTA (ensure ...

Type: Nextflow

Creators: Kisaru Liyanage, Matthew Downton

Submitter: Kisaru Liyanage

Stable

Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics, with updates November 2024.

Workflow inputs: reads as fastqsanger.gz (not fastq.gz), and primary assembly.fasta. (To change reads format: click on the pencil icon next to the file in the Galaxy history, then "Datatypes", then set "New type" as fastqsanger.gz). Note: the reads should be those that were used for the assembly (i.e., the filtered/cleaned reads), not the raw reads.

What it does: ...

Type: Galaxy

Creators: Kate Farquharson, Gareth Price, Simon Tang, Anna Syme

Submitters: Johan Gustafsson, Anna Syme

DOI: 10.48546/workflowhub.workflow.403.7

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

Inputs required: assembled-genome.fasta, hard-repeat-masked-genome.fasta, and (because this workflow maps known mRNA ...

Type: Galaxy

Creator: Luke Silver

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.881.5

Genome assembly workflow for nanopore reads, for TSI

Input:

  • Nanopore reads (can be in format: fastq, fastq.gz, fastqsanger, or fastqsanger.gz)

Optional settings to specify when the workflow is run:

  • [1] how many input files to split the original input into (to speed up the workflow). default = 0. example: set to 2000 to split a 60 GB read file into 2000 files of ~ 30 MB.
  • [2] filtering: min average read quality score. default = 10
  • [3] filtering: min read length. default = 200
  • [4] ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.1114.1

Scaffolding using HiC data with YAHS

This workflow has been created from a Vertebrate Genomes Project (VGP) scaffolding workflow.

Some minor changes have been made to better fit with TSI project data:

  • optional inputs of SAK info ...

Type: Galaxy

Creators: VGP Project, VGP, Galaxy

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.1054.1

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

Workflow information:

  • Input = genome.fasta.
  • Outputs = soft_masked_genome.fasta, hard_masked_genome.fasta, ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.875.3

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