Workflows

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595 Workflows visible to you, out of a total of 639
Lanczos SVD
Stable

Name: Lanczos SVD Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum4

Lanczos SVD for computing singular values needed to reach an epsilon of 1e-3 on a matrix of (150000, 150). The input matrix is generated synthetically. This application used dislib-0.9.0

Type: COMPSs

Creators: Fernando Vázquez-Novoa, Workflows and Distributed Computing

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.690.1

mRNA-Seq BY-COVID Pipeline: Analysis
Work-in-progress

Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA

Type: Galaxy

Creators: Iacopo Cristoferi, Helena Rasche, Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center

Submitter: Helena Rasche

mRNA-Seq BY-COVID Pipeline: Counts
Work-in-progress

This portion of the workflow produces sets of feature Counts ready for analysis by limma/etc.

Type: Galaxy

Creators: Iacopo Cristoferi, Helena Rasche, Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center

Submitter: Helena Rasche

GermlineStructuralV-nf

GermlineStructuralV-nf is a pipeline for identifying structural variant events in human Illumina short read whole genome sequence data. GermlineStructuralV-nf identifies structural variant and copy number events from BAM files using Manta, Smoove, and TIDDIT. Variants are then merged using SURVIVOR, ...

Type: Nextflow

Creators: Georgina Samaha, Marina Kennerson, Tracy Chew, Sarah Beecroft

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.431.1

PyCOMPSs Wordcount test, dividing input file in blocks, only Python dictionaries used as task parameters (run at MareNostrum IV)
Stable

Name: Word Count Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Wordcount is an application that counts the number of words for a given set of files.

To allow parallelism the file is divided in blocks that are treated separately and merged afterwards.

Results are printed to a Pickle binary file, so they can be checked using: python -mpickle result.txt

This example also shows how to manually add input or ...

Type: COMPSs

Creators: Javier Conejero, The Workflows and Distributed Computing Team (https://www.bsc.es/discover-bsc/organisation/scientific-structure/workflows-and-distributed-computing/)

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.687.1

dna-seq-varlociraptor
Stable

Snakemake workflow: dna-seq-varlociraptor

Snakemake GitHub actions status DOI

A ...

Type: Snakemake

Creators: Felix Mölder, David Lähnemann, Johannes Köster

Submitter: Johannes Köster

scRNAseq: Count and Load with starSOLO
Stable

Takes fastqs and reference data, to produce a single cell counts matrix into and save in annData format - adding a column called sample with the sample name.

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

mRNA-Seq BY-COVID Pipeline
Work-in-progress

Analyse Bulk RNA-Seq data in preparation for downstream Pathways analysis with MINERVA

Type: Galaxy

Creators: Iacopo Cristoferi, Helena Rasche

Submitter: Helena Rasche

PyCOMPSs Randomized SVD
Stable

Name: TruncatedSVD (Randomized SVD) Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum4

TruncatedSVD (Randomized SVD) for computing just 456 singular values out of a (3.6M x 1200) size matrix. The input matrix represents a CFD transient simulation of aire moving past a cylinder. This application used dislib-0.9.0

Type: COMPSs

Creators: Cristian Tatu, The Workflows and Distributed Computing Team (https://www.bsc.es/discover-bsc/organisation/scientific-structure/workflows-and-distributed-computing/)

Submitter: Cristian Tatu

Java COMPSs wordcount example (laptop run, files used as inputs)
Stable

Name: Java Wordcount Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Wordcount application. There are two versions of Wordcount, depending on how the input data is given.

Version 1

''Single input file'', where all the text is given in the same file and the chunks are calculated with a BLOCK_SIZE parameter.

Version 2

''Multiple input files'', where the text fragments are already in different files under ...

Type: COMPSs

Creators: Jorge Ejarque, The Workflows and Distributed Computing Team (https://www.bsc.es/discover-bsc/organisation/scientific-structure/workflows-and-distributed-computing/)

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.684.1

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