Workflows

What is a Workflow?
1307 Workflows visible to you, out of a total of 1392
Quality assessment, amplicon classification and functional prediction

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2.
In addition files are exported to their respective subfolders for easier data management in a later stage.

Steps:

  • Quality plots (FastQC)
  • NG-TAX 2 High-throughput Amplicon Analysis
  • PICRUSt 2 - Function prediction from marker gene sequences
  • Export module for ngtax

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Jasper Koehorst

DOI: 10.48546/workflowhub.workflow.154.2

Download
Longread 16S classification workflow
Work-in-progress

Workflow for quality assessment and taxonomic classification of amplicon long read sequences. In addition files are exported to their respective subfolders for easier data management in a later stage.

Inputs are expected to be basecalled fastq files

Steps:

  • NanoPlot read quality control, before and after filtering
  • fastplong read quality and length filtering
  • Emu abundance; species-level taxonomic abundance for full-length 16S read

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

(Hybrid) Metagenomics workflow
Work-in-progress

Workflow (hybrid) metagenomic assembly and binning

  • Workflow Illumina Quality:
  • Sequali (control)
  • hostile contamination filter
  • fastp (quality trimming)
  • Workflow Longread Quality:
  • NanoPlot (control)
  • fastplong (quality trimming)
  • hostile contamination filter
  • Kraken2 taxonomic classification of FASTQ reads
  • SPAdes/Flye (Assembly)
  • Medaka/PyPolCA (Assembly polishing)
  • QUAST (Assembly quality report)

(optional)

  • Workflow binnning
  • Metabat2/MaxBin2/SemiBin
  • Binette
  • BUSCO

...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke

Submitter: Bart Nijsse

DOI: 10.48546/workflowhub.workflow.367.2

Multisite phosphorylation of intrinsically disordered region of DVL facilitates Wnt signaling

KNIME workflow describing the analysis of mass spectrometry dataset related to the publication "Multisite phosphorylation of intrinsically disordered region of DVL facilitates Wnt signaling". Workflow was built using the KNIME software container environment, version 4.7.7, which can be created using "docker pull cfprot/knime:4.7.7" command in Docker.

Briefly, it contains the contaminants removal, log2 intensities transformation, data filtering, normalization, imputation of missing values and ...

Type: KNIME

Creator: Hana Plešingerová

Submitter: Hana Plešingerová

DOI: 10.48546/workflowhub.workflow.1870.1

Pipeface
Stable

Pipeface

Overview

Pipefaceee.

Nextflow pipeline to process long read ONT and/or pacbio HiFi data.

Pipeface's future hold's mitochondrial, STR, CNV and tandem repeat calling.

Workflow

Singleton

%%{init: {'theme':'dark'}}%% 
flowchart LR 

input_data("Input data: ONT fastq.gz and/or ONT fastq and/or ONT uBAM and/or pacbio HiFi uBAM") 
merging{{"Merge runs (if needed)"}} 
alignment{{"bam to fastq conversion (if needed), alignment,
...

Type: Nextflow

Creators: Leah Kemp, Andre Reis, Ira Deveson, Kisaru Liyanage, Matthew Downton, Hardip Patel, Kirat Alreja, This is a highly collaborative project, with many contributions from the Genomic Technologies Lab. Notably, Dr Andre Reis and Dr Ira Deveson are closely involved in the development of this pipeline. Optimisations involving DeepVariant and DeepTrio have been contributed by Dr Kisaru Liyanage and Dr Matthew Downton from the National Computational Infrastructure, with support from Australian BioCommons as part of the Workflow Commons project. Haploid-aware mode has been contributed by Dr Hardip Patel & Kirat Alreja from the National Centre for Indigenous Genomics. The installation and hosting of software used in this pipeline has and continues to be supported by the Australian BioCommons Tools and Workflows project (if89).

Submitter: Leah Kemp

DOI: 10.48546/workflowhub.workflow.1888.1

nf-core/scnanoseq

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

Type: Nextflow

Creators: Austyn Trull, Lara Ianov

Submitter: WorkflowHub Bot

Processed fastq QC
Stable

The workflow main goal is to quality trim reads of input fastq files and to remove adaptors. It can also run Biobloom tools and species detector in order to check for contamination. Finally it runs fastq QC to obtain quality check after trimming. The workflow was designed to be run in the SeqUIa (http://cfb.ceitec.muni.cz/sequia) application.

Type: Snakemake

Creators: None

Submitter: Nicolas Blavet

plant2human v1.1.0
Work-in-progress

plant2human workflow

GitHub last commit (branch) Status cwltool License Version ...

Type: Common Workflow Language

Creator: Sora Yonezawa

Submitter: Sora Yonezawa

DOI: 10.48546/workflowhub.workflow.1206.7

QuaCk

A Nextflow-based Quality Control tool used on assembled genomes and raw short and long reads data

Type: Nextflow

Creator: Henry Schober

Submitter: Henry Schober

DOI: 10.48546/workflowhub.workflow.1950.1

Settlement Delineation and Analysis
Stable

Description

The Settlement Delineation and Analysis (SDA) workflows generates a settlement network from geospatial settlement data. It can process geotiff and shapefile inputs and was originally designed to operate on the World Settlement Footprint dataset. Through multiple workflow stages, a settlement network is constructed, contracted (i.e. clustered) and ultimately analysed with centrality measures. The output shapefile stores the ...

Type: Docker

Creator: Lorenz Gruber

Submitter: Lorenz Gruber

DOI: 10.48546/workflowhub.workflow.1308.2

Powered by
 (v.1.17.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH