Workflows

What is a Workflow?
1236 Workflows visible to you, out of a total of 1317

DeepAnnotation can be used to perform genomic selection (GS), which is a promising breeding strategy for agricultural breeding. DeepAnnotation predicts phenotypes from comprehensive multi-omics functional annotations with interpretable deep learning framework. The effectiveness of DeepAnnotation has been demonstrated in predicting three pork production traits (lean meat percentage at 100 kg [LMP], loin muscle depth at 100 kg [LMD], back fat thickness at 100 kg [BF]) on a population of 1940 Duroc ...

Type: Python

Creators: Wenlong Ma, Weigang Zheng, Shenghua Qin, Chao Wang, Bowen Lei, Yuwen Liu

Submitter: Ma Wenlong

DOI: 10.48546/workflowhub.workflow.1732.1

Stable

High-throughput phenotyping is addressing the current bottleneck in phenotyping within breeding programs. Imaging tools are becoming the primary resource for improving the efficiency of phenotyping processes and providing large datasets for genomic selection approaches. The advent of AI brings new advantages by enhancing phenotyping methods using imaging, making them more accessible to breeding programs. In this context, we have developed an open Python workflow for analyzing morphology, colour ...

Work-in-progress

Modified workflow to perform Voronoi segmentation, based on https://usegalaxy.eu/published/workflow?id=23030421cd9fcfb2.

Input requirements:

  • RA: -- right ascension in degrees as a float number.
  • Dec: -- Declination in degrees as a float number
  • Radius: -- the radius of the cone to be queried in arcminutes as a float number
  • Pixel size: -- the size of the pixel in arcseconds
  • Band: -- the band (channel) of the image: g, r, z, i

Type: Galaxy

Creators: Andrei Variu, Riccardo Massei, Even Moa Myklebust

Submitter: Andrei Variu

Type: Snakemake

Creators: None

Submitter: Sanjay Nagi

Code for the high risk autism phenotype paper

MIT license

This repository implements a fully reproducible pipeline for the autism signature project. It uses invoke tasks and a Docker container for consistent, cross-platform execution.

The entire workflow—data fetching, processing, and figure generation—can be reproduced in a few commands. Much of the code in this repo originated from [ASD ...

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: Austyn Trull, Lara Ianov

Submitter: WorkflowHub Bot

Stable

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite with ...

Type: Nextflow

Creators: Harshil Patel, Phil Ewels, Rickard Hammarén

Submitter: WorkflowHub Bot

GitHub Actions CI Status GitHub Actions Linting Status AWS CI ...

Type: Nextflow

Creators: Gisela Gabernet, Simon Heumos, Alexander Peltzer

Submitter: WorkflowHub Bot

Decontamination (foreign contaminants and mitochondrial sequences) of a genome assembly after the final scaffolding step. Uses Kraken2 to identify foreign contaminants and Blast to identify mitochondrial sequences. Part of the VGP Suite.

Type: Galaxy

Creator: Nadolina Brajuka

Submitter: WorkflowHub Bot

Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

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