Workflows

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677 Workflows visible to you, out of a total of 726
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

Randomized SVD
Stable

Name: TruncatedSVD (Randomized SVD) Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

TruncatedSVD (Randomized SVD) for computing just 456 singular values out of a (4.5M x 850) size matrix. The input matrix represents a CFD transient simulation of air moving past a cylinder. This application used dislib-0.9.0

Type: COMPSs

Creator: Cristian Tatu

Submitter: Cristian Tatu

mettannotator
Stable

Nextflow run with docker run with singularity

mettannotator

Type: Nextflow

Creators: Tatiana Gurbich, Martin Beracochea

Submitter: Martin Beracochea

allele-based-pathogen-identification/main

Microbiome - Variant calling and Consensus Building

Type: Galaxy

Creators: Engy Nasr, Bérénice Batut, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1063.2

gene-based-pathogen-identification/main

Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building

Type: Galaxy

Creators: Engy Nasr, Bérénice Batut, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1062.1

nanopore-pre-processing/main

Microbiome - QC and Contamination Filtering

Type: Galaxy

Creators: Bérénice Batut, Engy Nasr, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1061.1

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