Workflows

What is a Workflow?
297 Workflows visible to you, out of a total of 320
Work-in-progress

Development Reads2Map

Reads2Map

Reads2Map presents a collection of WDL workflows to build linkage maps from sequencing reads. Each workflow release is described in the [Read2Map releases ...

Type: Workflow Description Language

Creator: Cristiane Taniguti

Submitter: Cristiane Taniguti

DOI: 10.48546/workflowhub.workflow.410.1

Work-in-progress

Development Reads2Map

Reads2Map

Reads2Map presents a collection of WDL workflows to build linkage maps from sequencing reads. Each workflow release is described in the [Read2Map releases ...

Type: Workflow Description Language

Creator: Cristiane Taniguti

Submitter: Cristiane Taniguti

DOI: 10.48546/workflowhub.workflow.409.1

Stable

This Galaxy-E workflow was made from the "Cleaning GBIF data for the use in biogeography" tutorial and allows to:

  • Use CoordinateCleaner to automatically flag problematic records
  • Use GBIF provided meta-data to improve coordinate quality, tailored to your downstream analyses
  • Use automated cleaning algorithms of CoordinateCleaner to identify problematic contributing datasets
  • Visualize data ...

Type: Galaxy

Creator: Yvan Le Bras

Submitter: Yvan Le Bras

DOI: 10.48546/workflowhub.workflow.404.1

Introduction

vibbits/rnaseq-editing is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation followed by a prediction step of editing sites using RDDpred.

The pipeline is largely based on the nf-core RNAseq pipeline.

The initial nf-core pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable ...

Type: Nextflow

Creators: None

Submitter: Alexander Botzki

Work-in-progress

Workflow for Metagenomics from bins to metabolic models (GEMs)

Summary

  • Prodigal gene prediction
  • CarveMe genome scale metabolic model reconstruction
  • MEMOTE for metabolic model testing
  • SMETANA Species METabolic interaction ANAlysis

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

All tool CWL files and other workflows can be found here: Tools: https://gitlab.com/m-unlock/cwl Workflows: https://gitlab.com/m-unlock/cwl/workflows

**How ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

Workflow for Metagenomics binning from assembly

Minimal inputs are: Identifier, assembly (fasta) and a associated sorted BAM file

Summary

  • MetaBAT2 (binning)
  • MaxBin2 (binning)
  • SemiBin (binning)
  • DAS Tool (bin merging)
  • EukRep (eukaryotic classification)
  • CheckM (bin completeness and contamination)
  • BUSCO (bin completeness)
  • GTDB-Tk (bin taxonomic classification)

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

**All tool CWL ...

Type: Common Workflow Language

Creators: Jasper Koehorst, Bart Nijsse

Submitter: Jasper Koehorst

Workflow Kallisto RNAseq

(pseudoalignment on transcripts)

All tool CWL files and other workflows can be found here:
Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl
Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows

How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

- deprecated -

Workflow for sequencing with ONT Nanopore, from basecalling to assembly.

  • Guppy (basecalling of raw reads)
  • MinIONQC (quality check)
  • FASTQ merging from multi into one file
  • Kraken2 (taxonomic classification)
  • Krona (classification visualization)
  • Flye (de novo assembly)
  • Medaka (assembly polishing)
  • QUAST (assembly quality reports)

All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl Workflows: ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Jasper Koehorst

Stable

Joint multi-omics dimensionality reduction approaches for CAKUT data using peptidome and proteome data

Brief description In (Cantini et al. 2020), Cantini et al. evaluated 9 representative joint dimensionality reduction (jDR) methods for multi-omics integration and analysis and . The methods are Regularized Generalized Canonical Correlation Analysis (RGCCA), Multiple co-inertia analysis (MCIA), Multi-Omics Factor Analysis (MOFA), Multi-Study Factor Analysis (MSFA), iCluster, Integrative NMF ...

Type: Snakemake

Creators: Ozan Ozisik, Juma Bayjan, Cenna Doornbos, Friederike Ehrhart, Matthias Haimel, Laura Rodriguez-Navas, José Mª Fernández, Eleni Mina, Daniël Wijnbergen

Submitter: Juma Bayjan

Stable

For integrative analysis of CAKUT multi-omics data DIABLO method of the mixOmics package (version 6.10.9. Singh et. al. 2019) was used with sPLS-DA (sparse Partial Least Squares Discriminant Analysis Discriminant Analysis) and PLS-DA classification.

Type: Snakemake

Creators: Juma Bayjan, Ozan Ozisik, Cenna Doornbos, Friederike Ehrhart

Submitter: Juma Bayjan

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