metaGOflow: A workflow for marine Genomic Observatories' data analysis

An EOSC-Life project

The workflows developed in the framework of this project are based on pipeline-v5 of the MGnify resource.

This branch is a child of the pipeline_5.1 branch that contains all CWL descriptions of the MGnify ...

ZARP

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Introduction

katdetectr is an R package for the detection, characterization and visualization of localized hypermutated regions, often referred to as kataegis.

Please see the Application Note (under submission) for additional background, details and performance evaluations of katdetectr.

The general workflow of katdetectr can be summarized as follows:

1. Import of genomic variants; VCF, MAF or VRanges objects.
2. Detection ...

MultiAffinity enables the study of how gene dysregulation propagates on a multilayer network on a disease of interest, uncovering key genes. Find the detailed documentation for the tool here.

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular interaction ...

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WRF/EMEP Linear Workflow

Example Common Workflow Language (CWL) workflow and tool descriptors for running the Weather Research and Forecase (WRF) and EMEP models.

This workflow is designed for a single model domain. Example datasets for testing this workflow can be downloaded from Zenodo.

Requirements:

• docker or singularity
• conda
• cwltool
• Toil - optional, useful for running on HPC or distributed computing systems

CWL / Toil Installation:

The workflow runner (either cwltool, or ...

Workflow for LongRead Quality Control and Filtering

• NanoPlot (read quality control) before and after filtering
• Filtlong (read trimming)
• Kraken2 taxonomic read classification before and after filtering
• Minimap2 read filtering based on given references

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

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

**How to setup and use an UNLOCK ...

Workflow for Illumina Quality Control and Filtering

Multiple paired datasets will be merged into single paired dataset.

Summary:

• FastQC on raw data files
• fastp for read quality trimming
• BBduk for phiX and (optional) rRNA filtering
• Kraken2 for taxonomic classification of reads (optional)
• BBmap for (contamination) filtering using given references (optional)
• FastQC on filtered (merged) data

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