Workflows

What is a Workflow?
1187 Workflows visible to you, out of a total of 1268
nf-core/metatdenovo

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Type: Nextflow

Creators: Danilo Di Leo, Emelie Nilsson & Daniel Lundin

Submitter: WorkflowHub Bot

Use Case 4: Identify the Tissue Activity for a TF based on its Targets

The workflow starts with selecting KLF4 as the search term. Gene sets with set labels containing KLF4 were queried from Enrichr[1]. Identified matching terms from the ENCODE TF ChIP-seq 2015[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ENCODE_TF_ChIP-seq_2015. Identified matching terms from the ChEA 2022[4] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ChEA_2022. Identified ...

Type: Unrecognized workflow type

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1239.2

Use Case 5: Small Molecules to Induce a Biological Process

The workflow starts with selecting Autophagy as the search term. Gene sets with set labels containing Autophagy were queried from Enrichr[1]. Identified matching terms from the MGI Mammalian Phenotype Level 4 2019[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for MGI_Mammalian_Phenotype_Level_4_2019. All the identified gene sets were combined using the union set operation. Reversers and mimickers from over 1 million signatures were identified ...

Type: Unrecognized workflow type

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1240.2

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

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

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