TRE-FX
OverviewTRE-FX is assembling leading technology providers from ELIXIR-UK and HDR UK, with three TRE providers and two leading analysis platforms to show through a real reference implementation how we can use secure Research Objects to move between TREs while still supporting the Five Safes principles that govern and protect patient data; all overseen by patient representatives.
Space: Independent Teams
SEEK ID: https://workflowhub.eu/projects/129
Funding codes:- MC_PC_23007
Public web page: https://trefx.uk/
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team start date: 1st Mar 2023
Team end date: 31st Oct 2023
Related items
Teams: TRE-FX
Organizations: University of Nottingham
Teams: IBISBA Workflows, GalaxyProject SARS-CoV-2, BioBB Building Blocks, Common Workflow Language (CWL) community, BioExcel Best Practice Guides, Specimen Data Refinery, FAIR Computational Workflows, Vertebrate Genomes Pipelines in Galaxy, TRE-FX, EuroScienceGateway, Biodiversity Genomics Europe (general), BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection
Organizations: The University of Manchester
https://orcid.org/0000-0001-9842-9718
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, Genomics Coordination Center, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, EuroScienceGateway, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC
Web page: Not specified
rquest-omop-worker-workflows
Source for workflow definitions for the open source RQuest OMOP Worker tool developed for Hutch/TRE-FX
Note: ARM workflows are currently broken. x86 ones work.
Inputs
### Body Sample input payload:
{
"task_id": "job-2023-01-13-14: 20: 38-",
"project": "",
"owner": "",
"cohort": {
"groups": [
{
"rules": [
{
"varname": "OMOP",
"varcat": "Person",
"type": "TEXT",
"oper": "=",
"value": "8507"
}
],
"rules_oper": "AND"
}
],
"groups_oper": "OR"
},
"collection":
...
Type: Common Workflow Language
Creator: Vasiliki Panagi
Submitters: Stian Soiland-Reyes, Vasiliki Panagi, Jon Couldridge
