Workflows
What is a Workflow?Filters
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.
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.
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
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 ...
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
...
Exome SAMtools Workflow
Exome Alignment Workflow
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 ...
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