Workflows

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831 Workflows visible to you, out of a total of 904
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

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, Changlin Ke

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

RASflow: RNA-Seq Analysis Snakemake Workflow
Stable

RASflow: RNA-Seq Analysis Snakemake Workflow

RASflow is a modular, flexible and user-friendly RNA-Seq analysis workflow.

RASflow can be applied to both model and non-model organisms. It supports mapping RNA-Seq raw reads to both genome and transcriptome (can be downloaded from public database or can be homemade by users) and it can do both transcript- and gene-level Differential Expression Analysis (DEA) when transcriptome is used as mapping reference. It requires little programming skill for ...

Type: Snakemake

Creator: Xiaokang Zhang

Submitter: Xiaokang Zhang

MGnify raw reads taxonomic profiling pipeline
Stable

The containerised pipeline for profiling shotgun metagenomic data is derived from the MGnify pipeline raw-reads analyses, a well-established resource used for analyzing microbiome data. Key components:

  • Quality control and decontamination
  • rRNA and ncRNA detection using Rfam database
  • Taxonomic classification of SSU and LSU regions
  • Abundance analysis with mOTUs

Type: Nextflow

Creators: Ekaterina Sakharova, Martin Beracochea

Submitter: Ekaterina Sakharova

WOMBAT-Pipelines
Work-in-progress

Introduction

wombat-p pipelines is a bioinformatics analysis pipeline that bundles different workflow for the analysis of label-free proteomics data with the purpose of comparison and benchmarking. It allows using files from the proteomics metadata standard SDRF.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses ...

Type: Nextflow

Creators: Veit Schwämmle, Magnus Palmblad

Submitters: Laura Rodriguez-Navas, José Mª Fernández

GRAVI: Gene Regulatory Analysis using Variable Inputs
Work-in-progress

GRAVI: Gene Regulatory Analysis using Variable Inputs

This is a snakemake workflow for:

  1. Performing sample QC
  2. Calling ChIP peaks
  3. Performing Differential Binding Analysis
  4. Comparing results across ChIP targets

The minimum required input is one ChIP target with two conditions.

Full documentation can be found here

Snakemake Implementation

The basic workflow is written snakemake, requiring at least v7.7, and can be called using the following ...

Type: Snakemake

Creator: Stevie Pederson

Submitter: Stevie Pederson

DOI: 10.48546/workflowhub.workflow.443.1

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