Workflows

What is a Workflow?
834 Workflows visible to you, out of a total of 910
Use Case 6: CFDE Knowledge about a Variant

The workflow starts with selecting chr10:g.3823823G>A as the search term. The closest gene to the variant was found using MyVariant.info[1]. RNA-seq-like LINCS L1000 Signatures[3] which mimick or reverse the the expression of KLF6 were visualized. Median expression of KLF6 was obtained from the GTEx Portal[8] using the portal's API. To visualize the scored tissues, a vertical bar plot was created Fig..

  1. Lelong, S. et al. BioThings SDK: a toolkit for building high-performance data APIs in ...

Type: Unrecognized workflow type

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1241.2

Settlement Delineation and Analysis
Stable

Description

The Settlement Delineation and Analysis (SDA) workflows generates a settlement network from geospatial settlement data. It can process geotiff and shapefile inputs and was originally designed to operate on the World Settlement Footprint dataset. Through multiple workflow stages, a settlement network is constructed, contracted (i.e. clustered) and ultimately analysed with centrality measures. The output shapefile stores the ...

Type: Unrecognized workflow type

Creator: Lorenz Gruber

Submitter: Lorenz Gruber

DOI: 10.48546/workflowhub.workflow.1308.1

nf-core/phyloplace

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creator: Daniel Lundin

Submitter: WorkflowHub Bot

nf-core/multiplesequencealign

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: Luisa Santus, Jose Espinosa Carrasco

Submitter: WorkflowHub Bot

ERGA-BGE Genome Report ANNOT analyses
Stable

The workflow requires the user to provide:

  • ENSEMBL link address of the annotation GFF3 file
  • ENSEMBL link address of the assembly FASTA file
  • NCBI taxonomy ID
  • BUSCO lineage
  • OMArk database

Thw workflow will produce statistics of the annotation based on AGAT, BUSCO and OMArk.

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.1096.1

DTC52 from Gitlab
Work-in-progress

CWL + RO-Crate Workflow Descriptions

This repository stores computational workflows described using the Common Workflow Language (CWL) and enriched with metadata using Research Object Crate (RO-Crate) conforming to the Workflow Run RO-Crate profile.

Each workflow is contained in its own directory (e.g., WF5201, WF6101, ...). Inside each workflow directory you will typically find at least:

  • The CWL workflow definition (with the same name as the directory, e.g., WF5201.cwl). ...

Type: Common Workflow Language

Creator: Marco Salvi

Submitter: Raül Sirvent

DTC61 from Gitlab
Work-in-progress

CWL + RO-Crate Workflow Descriptions

This repository stores computational workflows described using the Common Workflow Language (CWL) and enriched with metadata using Research Object Crate (RO-Crate) conforming to the Workflow Run RO-Crate profile.

Each workflow is contained in its own directory (e.g., WF5201, WF6101, ...). Inside each workflow directory you will typically find at least:

  • The CWL workflow definition (with the same name as the directory, e.g., WF5201.cwl). ...

Type: Common Workflow Language

Creator: Marco Salvi

Submitter: Raül Sirvent

tcga-data-nf
Work-in-progress

Workflow to download and prepare TCGA data.

The workflow divides the process of generating Gene Regulatory networks from TCGA cancer data in three steps:

  1. Downloading the raw data from GDC and saving the rds/tables needed later
  2. Preparing the data. This step includes filtering the data, normalizing it...
  3. Analysis of gene regulatory networks

Type: Nextflow

Creator: Viola Fanfani

Submitter: Viola Fanfani

PVGA

PVGA is a powerful virus-focused assembler that does both assembly and polishing. For virus genomes, small changes will lead to significant differences in terms of viral function and pathogenicity. Thus, for virus-focused assemblers, high-accuracy results are crucial. Our approach heavily depends on the input reads as evidence to produce the reported genome. It first adopts a reference genome to start with. We then align all the reads against the reference genome to get an alignment graph. After ...

Type: Python

Creators: None

Submitter: Zhi Song

nf-core/raredisease

GitHub Actions CI Status

GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creator: Clinical Genomics Stockholm

Submitter: WorkflowHub Bot

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