Workflows

What is a Workflow?
738 Workflows visible to you, out of a total of 793
nf-core/metapep

From metagenomes to peptides

Type: Nextflow

Creators: Sabrina Krakau, Leon Kuchenbecker and Till Englert

Submitter: WorkflowHub Bot

clinicalmp-database-generation/main

The workflow begins with the Database Generation process. The Galaxy-P team has developed a workflow that collects protein sequences from known disease-causing microorganisms to build a comprehensive database. This extensive database is then refined into a smaller, more relevant dataset using the Metanovo tool.

Type: Galaxy

Creator: Subina Mehta

Submitter: WorkflowHub Bot

plant2human workflow
Work-in-progress

plant2human workflow ~ structural similarity vs. sequence similarity ~

GitHub last commit (branch) Status cwltool License ...

Type: Common Workflow Language

Creator: Sora Yonezawa

Submitter: Sora Yonezawa

DOI: 10.48546/workflowhub.workflow.1206.3

Test at SC24
No description specified

Type: COMPSs

Creator: Daniele Lezzi

Submitter: Daniele Lezzi

Ecoregionalization workflow (Part 2)

Second part of the ecoregionalization

This workflow allows you to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.

The workflow is intended for processing occurrence data, which should include latitude, longitude and species presence or absence. You can use example test data available with the workflow, highlighting a use case centered on the Dumont d'Urville sea region and benthic invertebrates. The primary goal of ...

Type: Galaxy

Creator: Pauline Seguineau

Submitter: Pauline Seguineau

Ecoregionalization workflow (Part 1)

Part 1 of ecoregionalization workflow

This workflow allows you to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.

The workflow is intended for processing occurrence data, which should include latitude, longitude and species presence or absence. You can use example test data available with the workflow, highlighting a use case centered on the Dumont d'Urville sea region and benthic invertebrates. The primary goal of ...

Type: Galaxy

Creator: Pauline Seguineau

Submitter: Pauline Seguineau

Fgenesh annotation -TSI

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

Inputs required: assembled-genome.fasta, hard-repeat-masked-genome.fasta, and (because this workflow maps known mRNA ...

Type: Galaxy

Creator: Luke Silver

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.881.5

pseudobulk-worflow-decoupler-edger/main

This workflow uses the decoupler tool in Galaxy to generate pseudobulk counts from an annotated AnnData file obtained from scRNA-seq analysis. Following the pseudobulk step, differential expression genes (DEG) are calculated using the edgeR tool. The workflow also includes data sanitation steps to ensure smooth operation of edgeR and minimizing potential issues. Additionally, a Volcano plot tool is used to visualize the results after the DEG analysis.

Type: Galaxy

Creators: Diana Chiang Jurado, Pavankumar Videm, Pablo Moreno

Submitter: WorkflowHub Bot

Proximity interactomes of human PRICKLE1, PRICKLE2 and PRICKLE3.

KNIME workflow describing the analysis of mass spectrometry dataset related to the publication "Armed with PRICKLE(3)s: Stabilizing WNT/PCP complexes against RNF43-mediated ubiquitination". Workflow was built using the KNIME software container environment, version 4.7.7a, which can be created using "docker pull cfprot/knime:4.7.7a" command in Docker. The input data for the KNIME workflow (the report.tsv from DIA-NN) can be found on PRIDE repository under the identifier PXD057854.

Type: KNIME

Creators: Kristina Gomoryova, David Potěšil

Submitter: Kristina Gomoryova

DOI: 10.48546/workflowhub.workflow.1202.1

ONT Artificial Deletion Filter-Delter

ONT Artificial Deletion Filter-Delter

A tool to filter short artificial deletion variations by Oxford Nanopore Technologies (ONT) R9 and R10 flow cells and chemistries.

Requirements

The tool has been tested on Ubuntu 20.04 with 256GB RAM, 64 CPU cores and a NVIDIA GPU with 48GB RAM. The minimal requirements should be >= 64GB RAM and a NVIDIA GPU with >= 8GB RAM. Other operating systems like Windows or Mac were not tested.

ONT softwares like Guppy, ...

Type: Snakemake

Creators: None

Submitter: Qiang Ye

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