Workflows

What is a Workflow?
817 Workflows visible to you, out of a total of 891
nf-core/references

help community build references

Type: Nextflow

Creator: @maxulysse

Submitter: WorkflowHub Bot

Connectome-based predictive modeling (CPM) with Python using Ray for parallel processing
Work-in-progress

Installation

Other than cloning this repository, you need to have bash installed (which is most likely the case if you use Linux, *BSD or even MacOS). For the Python code, the arguably easiest and cleanest way is to set up a Python virtual environment and install the dependencies there:

$ python3 -m venv ./hcp-suite-venv # Setup the virtual environment 
$ source ./hcp-suite-venv/bin/activate # Activate the virtual environment 
$ pip install pandas pingouin networkx nilearn nibabel ray
...

Type: Python

Creator: Tobias Bachmann

Submitter: Tobias Bachmann

DOI: 10.48546/workflowhub.workflow.1234.1

(Hybrid) Metagenomics workflow
Work-in-progress

Workflow (hybrid) metagenomic assembly and binning

  • Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
  • FastQC (control)
  • fastp (quality trimming)
  • kraken2 (taxonomy)
  • bbmap contamination filter
  • Workflow Longread Quality:
  • NanoPlot (control)
  • filtlong (quality trimming)
  • kraken2 (taxonomy)
  • minimap2 contamination filter
  • Kraken2 taxonomic classification of FASTQ reads
  • SPAdes/Flye (Assembly)
  • Pilon/Medaka/PyPolCA (Assembly polishing)
  • QUAST (Assembly ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke

Submitter: Bart Nijsse

ONTViSc (ONT-based Viral Screening for Biosecurity)
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

nf-core/methylseq

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creator: Phil Ewels

Submitter: WorkflowHub Bot

ONT Artificial Deletion Filter-Delter
Stable

ONT Artificial Deletion Filter-Delter

A tool to filter short artificial deletion variations by Oxford Nanopore Technologies (ONT) R9 and R10 flow cells and chemistries.

Requirements

The tool has been tested on Ubuntu 20.04 with 256GB RAM, 64 CPU cores and a NVIDIA GPU with 48GB RAM. The minimal requirements should be >= 64GB RAM and a NVIDIA GPU with >= 8GB RAM. Other operating systems like Windows or Mac were not tested.

ONT softwares like Guppy, ...

Type: Snakemake

Creator: Qiang Ye

Submitter: Qiang Ye

DOI: 10.48546/workflowhub.workflow.1205.2

GIMP Image Annotator

gimp-image-annotator

gimp-image-annotator or GIÀ, a lightweight GIMP plug-in to alllow for computer vision-assisted image annotation using the powerful GIMP selection toolbox.

Installation

Follow the guide here: https://en.wikibooks.org/wiki/GIMP/Installing_Plugins to find how to install GIMP plug-ins on your system, save the file image-annotator.py in GIMP's plug-in folder.

In GIMP v2.x, the plug-in system relies on deprecated python2. On Windows, a version of python2 is included in ...

Type: Plug-in

Creator: Kieran Atkins

Submitter: Kieran Atkins

DOI: 10.48546/workflowhub.workflow.1229.1

kmer-profiling-hifi-VGP1/main

VGP Workflow #1

This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.

Inputs

  • A collection of Hifi long reads in FASTQ format
  • k-mer length
  • Ploidy

Outputs

  • Meryl Database of kmer counts

...

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

kmer-profiling-hifi-trio-VGP2/main

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

nf-core/phaseimpute

Phasing and imputation pipeline

Type: Nextflow

Creators: Louis Le Nezet, Anabella Trigila

Submitter: WorkflowHub Bot

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