Workflows

What is a Workflow?
558 Workflows visible to you, out of a total of 602
fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex

This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.

Type: Galaxy

Creators: Lucille Delisle, Mehmet Tekman, Hans-Rudolf Hotz, Daniel Blankenberg, Wendi Bacon

Submitter: WorkflowHub Bot

Reference-based assembly with bacpage
Work-in-progress

bacpage{width=500}

This repository contains an easy-to-use pipeline for the assembly and analysis of bacterial genomes using ONT long-read or Illumina short-read technology.

Introduction

Advances in sequencing technology during the COVID-19 pandemic has led to massive increases in the generation of sequencing data. Many bioinformatics tools have been developed to analyze this data, but very few tools ...

Type: Workflow Description Language

Creators: None

Submitter: Nathaniel Matteson

Somatic-ShortV-nf
Work-in-progress

This is a Nextflow implementaion of the GATK Somatic Short Variant Calling workflow. This workflow can be used to discover somatic short variants (SNVs and indels) from tumour and matched normal BAM files following GATK's Best Practices Workflow. The workflowis currently optimised to run efficiently and at scale on the National Compute Infrastructure, Gadi.

Type: Nextflow

Creators: Nandan Deshpande, Tracy Chew, Cali Willet, Georgina Samaha

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.691.1

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

Powered by
 (v.1.14.1)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH