Collection of EC-Earth3 workflows running with Autosubmit 3, with and without task wrappers, for different Slurm-based HPC platforms. See the individual descriptions for further details.

This is an inclusive super-collection of workflows related to biodiversity and ecology. A big portion covers genome assembly of newly-sequenced species, using long reads (ONT or PacBio HiFi), possibly complemented by chromosome capture (typically HiC) for scaffolding, or/and by short reads (typically Illumina). However, it aims at collating all workflows related to ecology, biodiversity, biogeography, natural history, and related scientific areas, across the whole WorkflowHub and regardless of ...

Collection of CWL worflows for various epigenomic data types, including DNA methylation, chromatin accessibility and chromatin marks (ChIP-seq, Cut'n'Run, ACT-Seq).

A collection of image processing templates designed to support data collection and automated processing for Single Particle Analysis (SPA) in cryo-electron microscopy. The workflows range from simple pipelines—including movie alignment, CTF estimation, and quality assessment—to fully automated 2D and 3D processing. Please select the workflow that best suits your needs.

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be PacBio HiFi or ONT reads and Illumina 3-dimensional Chromatin Confirmation Capture (Hi-C) reads

Executing the workflows collection will output a scaffolded primary assembly and alternate contigs, with the complete QC analyses

Please run the workflows in order: WF0', WF1, WF2, WF3, WF4

'Notice there is one for HiFi, one for ONT, and one for Illumina (WGS or Hi-C). Run according to your data. ...

Workflows developed by or used by BY-COVID project.

Pipelines used by the genomes assembly teams part of the Biodiversity Genomics Europe project

https://biodiversitygenomics.eu/

EuCanImage FHIR ETL Implementation

This repository contains the ETL implementation for EuCanImage, encouraging semantic interoperability of the clinical data obtained in the studies by transforming it into a machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create the dictionaries following a FHIR compliant structure.

• Code Language is written in Python 3.11. ...

Collection of Galaxy workflows for generating results used for creating ERGA-BGE Reports

For a given genome, two workflows should be run: the assembly evaluation (ASM analyses), and the annotation evaluation (ANNOT analyses)

Depending on the kind of data used for the genome assembly, you should choose HiFi or ONT (Illumina) workflows for ASM analyses