Workflows

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738 Workflows visible to you, out of a total of 793
Python Protein MD Setup tutorial
Stable

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

Copyright & Licensing

This software has been developed in the [MMB ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.276.3

PyUtils
No description specified

Type: Pi

Creators: None

Submitter: Tina Tian

Formula

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Type: Python

Creators: None

Submitter: Tina Tian

Jupyter Notebook Protein MD Setup tutorial
Stable

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

Copyright & Licensing

This software has been developed in the [MMB ...

Type: Jupyter

Creators: Genís Bayarri, Adam Hospital

Submitters: Douglas Lowe, Genís Bayarri

DOI: 10.48546/workflowhub.workflow.120.6

WRF / EMEP Linear Workflow
Work-in-progress

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 ...

Type: Common Workflow Language

Creator: Douglas Lowe

Submitter: Douglas Lowe

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

Assembly and quantification metatranscriptome using metagenome data.

Version: see VERSION

Introduction

MetaGT is a bioinformatics analysis pipeline used for improving and quantification metatranscriptome assembly using metagenome data. The pipeline supports Illumina sequencing data and complete metagenome and metatranscriptome assemblies. The pipeline involves the alignment of metatranscriprome assembly to the metagenome assembly with further extracting CDSs, which are covered by ...

Type: Nextflow

Creators: Andrey Prjibelski, Varsha Kale, Anton Korobeynikov

Submitter: Varsha Kale

(Hybrid) Metagenomics workflow
Work-in-progress

Workflow (hybrid) metagenomic assembly and binning + GEMs

Accepts both Illumina and Long reads (ONT/PacBio)

Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)

  • Metabat2/MaxBin2/SemiBin
  • DAS Tool
  • CheckM ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

LongRead Quality Control and Filtering
Work-in-progress

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 ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Bart Nijsse

Workflow for Illumina Quality Control and Filtering
Stable

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 ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

MoMofy: Module for integrative Mobilome prediction
Work-in-progress

MoMofy

Module for integrative Mobilome prediction

Bacteria can acquire genetic material through horizontal gene transfer, allowing them to rapidly adapt to changing environmental conditions. These mobile genetic elements can be classified into three main categories: plasmids, phages, and integrons. Autonomous elements are those capable of excising themselves from the chromosome, reintegrating elsewhere, and potentially modifying the host's physiology. Small integrative elements like insertion ...

Type: Nextflow

Creators: Alejandra Escobar, Martin Beracochea

Submitter: Alejandra Escobar

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