Workflows

What is a Workflow?
738 Workflows visible to you, out of a total of 793
ReMM score

The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding variations (SNVs and small InDels) in the human genome (GRCh37) in terms of Mendelian diseases. This project updates the ReMM score for the genome build GRCh38 and combines GRCh37 and GRCh38 into one workflow.

Pre-requirements

Conda

We use Conda as software and dependency management tool. Conda installation guidelines can be found here:

https://conda.io/projects/conda/en/latest/user-guide/install/index.html ...

Type: Snakemake

Creator: Max Schubach

Submitter: Max Schubach

DOI: 10.48546/workflowhub.workflow.414.1

Mothra
Work-in-progress

Example workflow which allows the use of Mothra

Accepts (e.g.) these input files, bundled as a collection.

Type: Galaxy

Creators: None

Submitter: Oliver Woolland

RNAseq_UMG_SDumont_v1

RNAseq workflow UMG: Here we introduce a scientific workflow implementing several open-source software executed by Galaxy parallel scripting language in an high-performance computing environment. We have applied the workflow to a single-cardiomyocyte RNA-seq data retrieved from Gene Expression Omnibus database. The workflow allows for the analysis (alignment, QC, sort and count reads, statistics generation) of raw RNA-seq data and seamless integration of differential expression results into a ...

Type: Galaxy

Creator: Kary Ocaña

Submitter: Kary Ocaña

DOI: 10.48546/workflowhub.workflow.412.1

ParslRNA-seq Scientific Workflow

RNA-seq Scientific Workflow

Workflow for RNA sequencing using the Parallel Scripting Library - Parsl.

Reference: Cruz, L., Coelho, M., Terra, R., Carvalho, D., Gadelha, L., Osthoff, C., & Ocaña, K. (2021). Workflows Científicos de RNA-Seq em Ambientes Distribuídos de Alto Desempenho: Otimização de Desempenho e Análises de Dados de Expressão Diferencial de Genes. In Anais do XV Brazilian e-Science Workshop, p. 57-64. Porto Alegre: SBC. DOI: https://doi.org/10.5753/bresci.2021.15789 ...

Type: Unrecognized workflow type

Creators: Lucas Cruz, Luiz Gadelha, Kary Ocaña

Submitter: Kary Ocaña

DOI: 10.48546/workflowhub.workflow.411.1

SimulatedReads2Map
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

EmpiricalReads2Map
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

GTN Training - Antibiotic Resistance Detection
Stable

Workflow for the GTN training "Antibiotic resistance detection"

Type: Galaxy

Creators: Saskia Hiltemann, Willem de Koning

Submitter: Saskia Hiltemann

GBIF data Quality check and filtering workflow Feb-2020
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

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

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

Metagenomic GEMs from Assembly
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

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