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Workflows

What is a Workflow?

829 Workflows visible to you, out of a total of 902

GBIF data Quality check and filtering workflow Feb-2020

PNDB

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

Created: 18th Nov 2022 at 14:39

RNA sequencing data obtained from organisms with a reference genome and annotation followed by a prediction step of editing sites using RDDpred

VIB Bioinformatics Core

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

Created: 27th Jan 2022 at 10:44, Last updated: 4th Nov 2022 at 20:36

Metagenomic GEMs from Assembly

UNLOCK

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

Created: 7th Jul 2022 at 09:23, Last updated: 2nd Nov 2022 at 15:41

Metagenomic Binning from Assembly

UNLOCK

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

Download

Created: 15th Oct 2020 at 14:55, Last updated: 2nd Nov 2022 at 15:29

Kallisto RNAseq Workflow

UNLOCK

Workflow Kallisto RNAseq

(pseudoalignment on transcripts)

Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
kallisto

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

Created: 20th May 2022 at 11:10, Last updated: 2nd Nov 2022 at 15:26

Nanopore Guppy Basecalling Assembly Workflow

UNLOCK

(Show All)

- 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

Download

Created: 6th Jan 2022 at 07:36, Last updated: 2nd Nov 2022 at 15:03

EJP-RD WP13 case-study CAKUT momix analysis

EJPRD WP13 case-studies workflows

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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

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Created: 23rd Jun 2021 at 11:42, Last updated: 27th Oct 2022 at 17:39

EJP-RD WP13 case-study: CAKUT peptidome and miRNome data analysis using the DIABLO and PLS-DA methods from the mixOmics R package

EJPRD WP13 case-studies workflows

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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

Created: 20th Apr 2022 at 17:43, Last updated: 27th Oct 2022 at 17:38

EJP-RD WP13 case-study: CAKUT proteome, peptidome and miRNome data analysis using WikiPathways

EJPRD WP13 case-studies workflows

(Show All)

Stable

In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics datasets. For this, each of the three -omics datasets was first analyzed to identify differentially expressed elements, and pathways associated with the significant miRNA-protein links were detected. A miRNA-protein link is deemed significant, and may possibly be implying causality, if both a miRNA and its target are significantly differentially expressed.

The peptidome and ...

Type: Snakemake

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

Submitter: Juma Bayjan

Created: 20th Apr 2022 at 17:59, Last updated: 27th Oct 2022 at 16:16

PacBio HiFi genome assembly using hifiasm v2.1

Galaxy Australia, Australian BioCommons