Workflows

What is a Workflow?
814 Workflows visible to you, out of a total of 888
Galaxy Workflow for CNV Detection with CNVkit and Conversion to Beacon JSON Using cnv-vcf2json
Stable

This Galaxy workflow streamlines comprehensive copy number variation (CNV) analysis by integrating CNVkit’s robust detection capabilities with an efficient conversion step using cnv-vcf2json to format results into Beacon JSON. Designed for computational biologists and bioinformaticians, the workflow standardizes CNV identification and output formatting to enhance interoperability with Beacon networks. It is specifically optimized for use with mapped BAM files from the EGAD00001008392 synthetic ...

Type: Galaxy

Creators: Khaled Jum'ah, Krzysztof Poterlowicz

Submitter: Khaled Jum'ah

DOI: 10.48546/workflowhub.workflow.1314.1

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

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Type: Nextflow

Creator: Daniel Lundin

Submitter: WorkflowHub Bot

nf-core/multiplesequencealign

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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

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