Workflows

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736 Workflows visible to you, out of a total of 791
BY-COVID WP5 T5.2 Baseline Use Case
Work-in-progress

This publication corresponds to the Research Objects (RO) of the Baseline Use Case proposed in T.5.2 (WP5) in the BY-COVID project on “COVID-19 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection”.

Type: Quarto Markdown

Creators: Enrique Bernal-Delgado, Nina Van Goethem, Francisco Estupiñan-Romero, Marjan Meurisse, Javier González Galindo, Natalia Martínez-Lizaga, Santiago Royo-Sierra

Submitter: Marjan Meurisse

DOI: 10.48546/workflowhub.workflow.502.4

cocomico_wf_simulated

CoCoMiCo analyses on collections of simulated communities. Community: scatterplots and KW tests of cooperation and competition potentials, for each collection. Similarity: cooperation and competition potentials vs model similarity, defined as the Jaccard distance on sets of reactions. Added value: boxplots comparing the added value of models in communities.

Type: Common Workflow Language

Creators: None

Submitter: David James Sherman

Lysozyme in water full, no MPI
Stable

Lysozyme in water full COMPSs application

Type: COMPSs

Creator: Javier Conejero

Submitter: Raül Sirvent

Lysozyme in water, using dataset_small, data_persistence True
Stable

Lysozyme in water full COMPSs application, using dataset_small

Type: COMPSs

Creator: Rosa M. Badia

Submitter: Raül Sirvent

Lysozyme in water full (GitHub)
Stable

Lysozyme in water full COMPSs application

Type: COMPSs

Creator: Javier Conejero

Submitter: Raül Sirvent

Deepconsensus for Sequel2/2e subreads

deepconsensus 1.2 snakemake pipeline

This snakemake-based workflow takes in a subreads.bam and results in a deepconsensus.fastq

  • no methylation calls !

The metadata id of the subreads file needs to be: "m[numeric][numeric][numeric].subreads.bam"

Chunking (how many subjobs) and ccs min quality filter can be adjusted in the config.yaml

the checkpoint model for deepconsensus1.2 should be accessible like this: gsutil cp -r gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* ...

Type: Snakemake

Creators: None

Submitter: dan rick

CEITEC layer 1 workflow
Work-in-progress

The second-level complexity workflow is one among a collection of workflows designed to address tasks up to CTF estimation. In addition to the functionalities provided by the layer 0 workflow, this workflow aims to enhance the quality of acquisition images using quality protocols.

Quality control protocols

  • Movie max shift: automatic reject those movies whose frames move more than a given threshold. 

  • Tilt analysis: quality score based in the Power Spectrum Density (astigmatism and ...

Type: Scipion

Creators: None

Submitters: Daniel Marchan, Pablo Conesa

CRYOSPARC: acquire -> motionCorr -> ctf -> report
Work-in-progress

SPA workflow using cryosparc processing engine

Type: Unrecognized workflow type

Creators: None

Submitter: Radek Veverka

SCIPION: acquire -> motionCorr -> ctf -> report
Work-in-progress

The simplest workflow among a collection of workflows intended to solve tasks up to CTF estimation.

Type: Scipion

Creators: None

Submitter: Daniel Marchan

KMeans housing

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

KMEans for clustering the housing.csv dataset (https://github.com/sonarsushant/California-House-Price-Prediction/blob/master/housing.csv). This application used dislib-0.9.0

Type: COMPSs

Creator: Fernando Vázquez-Novoa

Submitters: Raül Sirvent, Fernando Vázquez-Novoa

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