Workflows

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

SNP-Calling Workflow
Work-in-progress

SNP-Calling

GATK Variant calling pipeline for genomic data using Nextflow

nextflow

Quickstart

Install Nextflow using the following command:

curl -s https://get.nextflow.io | bash

Index reference genome:

$ bwa index /path/to/reference/genome.fa

$ samtools faidx /path/to/reference/genome.fa

$ gatk CreateSequenceDictionary -R /path/to/genome.fa -O genome.dict

Launch the pipeline execution with ...

Type: Nextflow

Creators: None

Submitter: Jeffrey Detras

IGVreport-nf
Work-in-progress

IGVreport-nf

Description

Quickly generate [IGV .html ...

Type: Nextflow

Creators: Georgina Samaha, Tracy Chew

Submitter: Georgina Samaha

Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation
Work-in-progress

ROIforMSI

Source codes for manuscript "Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation"

"ExampleWorkflow.ipynb" is a methods document to demonstrate the workflow of our multimodal fusion-based spatial segmentation.

"Utilities.py" contains all the tools to implement our method.

"gui.py" and "registration_gui.py" are files to implement linear and nonlinear registration.

(Licence: GPL-3)

Type: Python

Creators: Ang Guo, Qian Luo

Submitter: Ang Guo

DOI: 10.48546/workflowhub.workflow.437.1

Trio Analysis
Stable

To discover causal mutations of inherited diseases it’s common practice to do a trio analysis. In a trio analysis DNA is sequenced of both the patient and parents. Using this method, it’s possible to identify multiple inheritance patterns. Some examples of these patterns are autosomal recessive, autosomal dominant, and de-novo variants, which are represented in the figure below. To elaborate, the most left tree shows an autosomal dominant inhertitance pattern where the offspring inherits a faulty ...

Type: Galaxy

Creator: Jasper Ouwerkerk

Submitter: Helena Rasche

DOI: 10.48546/workflowhub.workflow.363.2

Apis-wings-EU: A workflow for morphometric identification of honey bees from Europe
Stable

We present an R script that describes the workflow for analysing honey bee (Apis mellifera) wing shape. It is based on a large dataset of wing images and landmark coordinates available at Zenodo: https://doi.org/10.5281/zenodo.7244070. The dataset can be used as a reference for the identification of unknown samples. As unknown samples, we used data from Nawrocka et al. (2018), available at Zenodo: https://doi.org/10.5281/zenodo.7567336. Among others, the script can be used to identify the geographic ...

Type: R markdown

Creators: Andrzej Oleksa, Eliza Căuia, Adrian Siceanu, Zlatko Puškadija, Marin Kovačić, M. Alice Pinto, Pedro João Rodrigues, Fani Hatjina, Leonidas Charistos, Maria Bouga, Janez Prešern, Irfan Kandemir, Slađan Rašić, Szilvia Kusza, Adam Tofilski

Submitter: Adam Tofilski

DOI: 10.48546/workflowhub.workflow.422.1

pox-virus-amplicon/main

A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach

Type: Galaxy

Creators: Viktoria Isabel Schwarz, Wolfgang Maier

Submitter: WorkflowHub Bot

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