Workflows

What is a Workflow?
738 Workflows visible to you, out of a total of 793
MLme: Machine Learning Made Easy

This workflow represents the Default ML Pipeline for AutoML feature from MLme. Machine Learning Made Easy (MLme) is a novel tool that simplifies machine learning (ML) for researchers. By integrating four essential functionalities, namely data exploration, AutoML, CustomML, and visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. MLme serves as a valuable resource that empowers researchers of all technical levels to leverage ...

Type: Workflow Description Language

Creator: Akshay Akshay

Submitter: Akshay Akshay

DOI: 10.48546/workflowhub.workflow.571.1

ERGA Protein-coding gene annotation workflow

ERGA Protein-coding gene annotation workflow.

Adapted from the work of Sagane Joye:

https://github.com/sdind/genome_annotation_workflow

Prerequisites

The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: https://github.com/nextflow-io/nextflow/issues/1659.

conda v 23.7.3 ...

Type: Snakemake

Creator: Sagane Joye-Dind

Submitter: Tom Brown

DOI: 10.48546/workflowhub.workflow.569.1

polish-with-long-reads/main

Racon polish with long reads, x4

Type: Galaxy

Creator: Anna Syme

Submitter: WorkflowHub Bot

parallel-accession-download/main

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.

Type: Galaxy

Creators: Marius van den Beek, IWC

Submitter: WorkflowHub Bot

consensus-peaks/consensus-peaks-chip-sr

This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

chipseq-pe/main

This workflow takes as input a collection of paired fastqs. Remove adapters with cutadapt, map pairs with bowtie2. Keep MAPQ30 and concordant pairs. MACS2 for paired bam.

Type: Galaxy

Creators: Lucille Delisle, Lucille Delisle

Submitter: WorkflowHub Bot

chipseq-sr/main

This workflow takes as input a collection of fastqs (single reads). Remove adapters with cutadapt, map with bowtie2. Keep MAPQ30. MACS2 for bam with fixed extension or model.

Type: Galaxy

Creators: Lucille Delisle, Lucille Delisle

Submitter: WorkflowHub Bot

HiFi de novo genome assembly workflow
Stable

HiFi de novo genome assembly workflow

HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.

Please refer to the following documentation for detailed description of each workflow section:

  • [Adapter filtration and pre-assembly quality control ...

Type: Nextflow

Creators: Naga Kasinadhuni, Ziad Al-Bkhetan, Martha Zakrzewski, Kenneth Chan, Uwe Winter, Johan Gustafsson

Submitter: Johan Gustafsson

Apis-mellifera-wings-KZ: A workflow for morphometric identification of honey bees from Kazakhstan

We present an R script that describes the workflow for analysing honey bee (Apis mellifera) wing shape. It is based on a dataset of wing images and landmark coordinates available at Zenodo: https://doi.org/10.5281/zenodo.8128010. The dataset can be used as a reference for the identification of local bees from southern Kazakhstan, which most probably belong to the subspecies Apis mellifera pomonella. It was compared with data from Nawrocka et al. (2018), available at Zenodo: ...

Type: R markdown

Creators: Kamshat Temirbayeva, Aibyn Torekhanov, Ulzhan Nuralieva, Zhanar Sheralieva, Adam Tofilski

Submitter: Adam Tofilski

DOI: 10.48546/workflowhub.workflow.559.1

Galaxy Protein Conformational Transitions calculations tutorial
Stable

Protein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...

Type: Galaxy

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.558.1

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