Workflows

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834 Workflows visible to you, out of a total of 910
EuCanImage FHIR ETL Implementation VII: Breast Cancer MRI

EuCanImage FHIR ETL Implementation

This repository contains the ETL implementation for EuCanImage, encouraging semantic interoperability of the clinical data obtained in the studies by transforming it into a machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create the dictionaries following a FHIR compliant structure.

Type: Python

Creators: Aldar Cabrelles, https://github.com/EGA-archive/EuCanImage-FHIR

Submitter: Aldar Cabrelles

DOI: 10.48546/workflowhub.workflow.1159.1

PhysioNet kNN Kfold
Stable

Name: PhysioNet kNN Kfold Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

Kfold to evaluate kNN accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0

Type: COMPSs

Creator: Fernando Vázquez-Novoa

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.1123.2

Workflow 3: AMR - SeqSero2/SISTR
Work-in-progress

With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.

This pipeline is based on the work of the National Food Agency of Canada. Doi: 10.3389/fmicb.2020.00549

tool version license
SeqSero2 1.2.1 GNU GPL v2.0
...

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

Workflow 2: Sciensano
database database version
ResFinder 2022-07-19
CARD 2023-12-03

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

Workflow 4: Staramr
Work-in-progress

Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr.

Doi: 10.3390/microorganisms10020292

tool version license
staramr 0.8.0 Apache-2.0 license

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

Workflow 1: AbritAMR
tool version license
abritAMR 1.0.14 CC-BY-4.0

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

GADES reproducibility workflow
Stable

Article-GADES

This repository represents generating and benchmarking the results of the GADES package for Distance Matrix Calculation

Installation

git lfs install 
git clone https://github.com/lab-medvedeva/Article-GADES.git 
cd Article-GADES

Put the Real datasets in the MEX format to the folder Datasets/Real.

Running benchmark using Docker Deployment

docker run --gpus all \ 
-v $PWD/Datasets:/workspace/Article-GADES/Datasets
...

Type: Docker

Creator: Pavel Akhtyamov

Submitter: Pavel Akhtyamov

DOI: 10.48546/workflowhub.workflow.1125.1

PhysioNet CascadeSVM Kfold

Name: PhysioNet CascadeCSVM Kfold Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

Kfold to evaluate CascadeCSVM accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0

Type: COMPSs

Creator: Fernando Vázquez-Novoa

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.1124.1

PhysioNet RF Kfold

Name: PhysioNet RF Kfold Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

Kfold to evaluate RandomForest accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0

Type: COMPSs

Creator: Fernando Vázquez-Novoa

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.1122.1

Genome assembly workflow for nanopore reads, for TSI

Genome assembly workflow for nanopore reads, for TSI

Input:

  • Nanopore reads (can be in format: fastq, fastq.gz, fastqsanger, or fastqsanger.gz)

Optional settings to specify when the workflow is run:

  • [1] how many input files to split the original input into (to speed up the workflow). default = 0. example: set to 2000 to split a 60 GB read file into 2000 files of ~ 30 MB.
  • [2] filtering: min average read quality score. default = 10
  • [3] filtering: min read length. default = 200
  • [4] ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.1114.1

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