Workflows

What is a Workflow?
1299 Workflows visible to you, out of a total of 1382

Microbiome - QC and Contamination Filtering

Associated Tutorial

This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: GTN Bot

Building an amplicon sequence variant (ASV) table from 16S data using DADA2

Associated Tutorial

This workflows is part of the tutorial Building an amplicon sequence variant (ASV) table from 16S data using DADA2, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: GTN Bot

GitHub Actions CI Status GitHub Actions Linting Status AWS CI ...

Type: Nextflow

Creator: Stephen Watts

Submitter: WorkflowHub Bot

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

Type: Nextflow

Creators: None

Submitter: WorkflowHub Bot

Domestication of new parts before cloning simulation

Add new parts to your sequences before the cloning simulation and interact with the database.

steps:

input: csv file (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.

seq_from_DB

  1. Extract the fragments associated with each constraint from the CSV file.
  2. Check if all fragments are ...

Type: Galaxy

Creators: None

Submitter: ramiz khaled

Generate annotated gb for fragments and add them to DB

Automatically generate annotated GenBank files for your fragments based on your constraints and store them in your database.

steps:

input: GenBank files : If your fragments are not in the database, you can generate GenBank files for each fragment to be used as input for the annotation workflow and then passed to the evaluate_manufacturability tool.

evaluate_manufacturability

  1. Set the constraints for the annotations. ...

Type: Galaxy

Creators: None

Submitter: ramiz khaled

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

Creators: None

Submitter: Louise Cordrie

Work-in-progress

Digitial Twin Component for Earthquakes (DTC-E5) WorkFlow 1 (WF7501) uses new data to create a multi-scale model of the Earth, which is used to update the REVEAL/CSEMv3 velocity model. The WF7501 workflow models an inversion-based update process for CSEMv3 (Computational Seismic Earth Model). Below is a simple explanation of the STEPs:

  • ST750101 - Data Catalog Update: Collects external data sources and updates the database for further processing.
  • ST750102 - Inversion Setup: Configures ...

Type: Common Workflow Language

Creators: Johannes Kemper, Marta Pienkowska, Andreas Fichtner, Christian Böhm, Scott Keating

Submitter: Johannes Kemper

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

Creators: None

Submitter: Rebecca Bruni

Stable

This workflow extracts protein-coding sequences from whole genome sequencing (WGS) data obtained from the European Nucleotide Archive (ENA). It automates the preprocessing, annotation, and selection of relevant protein sequences using tools such as Prokka, FASTA-to-Tabular, and pattern-based selection. The resulting dataset supports downstream analyses including comparative genomics, phylogenetics, and functional annotation.

Type: Galaxy

Creator: Crist John M. Pastor

Submitter: Crist John Pastor

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