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 ...

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 ...

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 ...

Reads2Map

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

Reads2Map

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

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 ...

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 ...

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 ...

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 ...

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