Workflows

What is a Workflow?
836 Workflows visible to you, out of a total of 912
nf-core/hlatyping

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Type: Nextflow

Creators: Christopher Mohr, Alexander Peltzer, Sven Fillinger

Submitter: WorkflowHub Bot

gSpreadComp

gSpreadComp: Streamlining Microbial Community Analysis for Resistance, Virulence, and Plasmid-Mediated Spread

Overview

gSpreadComp is a UNIX-based, modular bioinformatics toolkit designed to streamline comparative genomics for analyzing microbial communities. It integrates genome annotation, gene spread calculation, plasmid-mediated horizontal gene transfer (HGT) detection and resistance-virulence ranking within the analysed microbial community to help researchers identify potential ...

Type: Shell Script

Creator: Jonas Kasmanas

Submitter: Jonas Kasmanas

DOI: 10.48546/workflowhub.workflow.1340.3

COMPSs Matrix Multiplication resourceUsage profiling example MN5 MSIZE=20 BSIZE=768 7 Nodes total
Stable

COMPSs Matrix Multiplication resourceUsage profiling example.

MN5 MSIZE=20 BSIZE=768 7 Nodes (6 workers) (--num_nodes=7 --worker_in_master_cpus=0).

  • Total number of tasks: 20^3 = 8000
  • Maximum code parallelism: 20^2 = 400
  • Total cores: 112*6 = 672
  • Maximum utilisation: 400 / 112 = 3,57 Nodes

Overall stats from "pycompss inspect":

│ └── overall 
│ ├── matmul_tasks 
│ │ └── multiply 
│ │ ├── maxTime = 91,111 ms 
│ │ ├── executions = 8,000 
│ │ ├── avgTime = 84,839 ms 
│ │ └── minTime = 79,278 ms
...

Type: COMPSs

Creators: Raül Sirvent, Rosa M Badia

Submitter: Raül Sirvent

Matrix Multiplication – resource usage visualization

Application that perform the multiplication between matrices. In this experiment, a new profiling visualization is available, showing the resource usage such as CPU, memory, data read and written to disk, and data sent and received over the network.

Type: COMPSs

Creators: Raül Sirvent, Nicolò Giacomini

Submitter: Nicolò Giacomini

tissue-microarray-analysis/main

Complete multiplex tissue image (MTI) analysis pipeline for tissue microarray (TMA) data imaged using cyclic immunofluorescence: Performs illumination correction, stitching and registration, and tissue microarray segmentation. Tissue-segmented images undergo nuclear segmentation, cell/nuclei feature quantification (mean marker intensities, cell coordinates, and morphological features), and cell phenotyping. Produces outputs that are compatible with downstream single-cell/spatial analysis and ...

Type: Galaxy

Creator: Cameron Watson

Submitter: WorkflowHub Bot

nf-core/fastquorum

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Type: Nextflow

Creator: Nils Homer

Submitter: WorkflowHub Bot

Reproducible functional connectivity signature confers high risk of autism spectrum disorder in a subset of individuals

Code for the high risk autism phenotype paper

MIT license

Much of the code in this repo originated from ASD High Risk Endophenotype Code Supplement and was written by Sebastian Urchs and Hien Nguyen.

Data availability

All data to reproduce the analysis can be downloaded from DOI ...

Type: R markdown

Creators: Natasha Clarke, Lune Bellec

Submitter: Natasha Clarke

DOI: 10.48546/workflowhub.workflow.1336.1

nf-core/rnavar

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Type: Nextflow

Creators: @praveenraj2018 , @praveenraj2018

Submitter: WorkflowHub Bot

[DTC-E5] WF7501: Full waveform inversion of Earth model or Earth-DT
Work-in-progress

Digitial Twin Component for Earthquakes (DTC-E) WorkFlow 1 (WF7501) uses new data to create a multi-scale model of the Earth, which is used to update the REVEAL/CSEMv3 velocity model. The WF7501 workflow models an inversion-based update process for CSEMv3 (Computational Seismic Earth Model). Below is a simple explanation of the STEPs:

  • ST750101 - Data Catalog Update: Collects external data sources and updates the database for further processing.
  • ST750102 - Inversion Setup: Configures ...

Type: Common Workflow Language

Creator: Johannes Kemper

Submitter: Johannes Kemper

[DTC-E5] WF7502: Synthetic shaking simulation or Event-DT
Work-in-progress

Digitial Twin Component for Earthquakes (DTC-E) WorkFlow 2 (WF7502) generates synthetic shaking simulations (shakemaps) for seismic sources at different time scales, and automatically incorporates new data as it becomes available.

The workflow consists of multiple steps (ST), datasets (DT), and software services (SS). Below is a simplified breakdown:

Data Ingestion & Preprocessing

  • ST750201: Assimilates real-time earthquake data from external sources.
  • ST750202: Extracts earthquake ...

Type: Common Workflow Language

Creators: Johannes Kemper, Cedric Bhihe, Georgina Díez

Submitter: Johannes Kemper

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