Workflows

What is a Workflow?
1299 Workflows visible to you, out of a total of 1382

Protein-ligand complex parameterization

Parameterizes an input protein (PDB) and ligand (SDF) file prior to molecular dynamics simulation with GROMACS.

This is a simple workflow intended for use as a subworkflow in more complex MD workflows. It is used as a subworkflow by the GROMACS MMGBSA and dcTMD workflows.

Type: Galaxy

Creator: Simon Bray

Submitter: WorkflowHub Bot

Stable

This workflow extracts 5 different time periods e.g. January- June 2019, 2020 and 2021, July-December 2019 and 2020 over a single selected location. Then statistics (mean, minimum, maximum) are computed. The final products are maximum, minimum and mean.

Type: Galaxy

Creators: None

Submitter: Anne Fouilloux

DOI: 10.48546/workflowhub.workflow.251.1

Stable

Description

The workflow takes an input file with Cancer Driver Genes predictions (i.e. the results provided by a participant), computes a set of metrics, and compares them against the data currently stored in OpenEBench within the TCGA community. Two assessment metrics are provided for that predictions. Also, some plots (which are optional) that allow to visualize the performance of the tool are generated. The workflow consists in three standard steps, defined by OpenEBench. The tools needed ...

Type: Nextflow

Creators: José Mª Fernández, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas

Submitter: Laura Rodriguez-Navas

Work-in-progress
No description specified

Type: Galaxy

Creators: None

Submitter: Paul Brack

Stable

Summary

This notebook shows how to integrate genomic and image data resources. This notebook looks at the question Which diabetes related genes are expressed in the pancreas?

Steps:

  • Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the genes.
  • Using the list of found genes, search in the Image Data Resource (IDR) for images linked to the genes, tissue and disease.

We use the intermine API and the IDR API

The notebook can be launched ...

Work-in-progress

atavide is a complete workflow for metagenomics data analysis, including QC/QA, optional host removal, assembly and cross-assembly, and individual read based annotations. We have also built in some advanced analytics including tools to assign annotations from reads to contigs, and to generate metagenome-assembled genomes in several different ways, giving you the power to explore your data!

atavide is 100% snakemake and conda, so you only need to install the snakemake workflow, and then ...

Type: Snakemake

Creators: None

Submitter: Rob Edwards

DOI: 10.48546/workflowhub.workflow.241.1

Stable

Exome SAMtools Workflow

Type: Nextflow

Creator: Laura Rodriguez-Navas

Submitter: Laura Rodriguez-Navas

Stable

Exome Alignment Workflow

Type: Common Workflow Language

Creator: Laura Rodriguez-Navas

Submitter: Laura Rodriguez-Navas

Stable

Summary

This notebook demonstrates how to retrieve metadata associated to the paper A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection and available in IDR at idr0094-ellinger-sarscov2. Over 300 compounds were used in this investigation. This notebook allows the user to calculate the half maximal inhibitory concentration (IC50) for ...

Type: Jupyter

Creators: Jean-Marie Burel, Andrea Zaliani

Submitter: Jean-Marie Burel

DOI: 10.48546/workflowhub.workflow.238.1

Work-in-progress

This is a genomics pipeline to do a single germline sample variant-calling, adapted from GATK Best Practice Workflow.

This workflow is a reference pipeline for using the Janis Python framework (pipelines assistant).

  • Alignment: bwa-mem
  • Variant-Calling: GATK HaplotypeCaller
  • Outputs the final variants in the VCF format.

Resources

This pipeline has been tested using the HG38 reference set, available on Google Cloud Storage through:

Type: Janis

Creators: Richard Lupat, Michael Franklin; Jiaan Yu; Juny Kesumadewi

Submitter: Richard Lupat

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