Workflows

What is a Workflow?
1236 Workflows visible to you, out of a total of 1317
workflow-2

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

workflow-0

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

workflow-1

Cloning simulation workflow for sequences present in DB

Run the GoldenGate cloning simulation for a list of constructs in a CSV file and interact with a 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 ...

Type: Galaxy

Creators: None

Submitter: ramiz khaled

[DTC-V3] WF5301: Lava flow
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

[DTC-E5] WF7501: Full waveform inversion of Earth model or Earth-DT
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

TAXAPUS - your eight-armed taxonomy assistant

qcif/taxapus is a modular, reproducible Nextflow workflow for the conservative taxonomy assignment to DNA sequences, designed for high-confidence, auditable results in biosecurity and biodiversity contexts. The workflow integrates multiple bioinformatics tools and databases, automates best-practice analysis steps, and produces detailed reports with supporting evidence for each taxonomic assignment.

Workflow Overview

The pipeline orchestrates a series of analytical steps, each encapsulated ...

Type: Nextflow

Creators: Magdalena Antczak, Cameron Hyde, Lanxi (Daisy) Li, Valentine Murigneux, Sarah Williams, Michael Thang, Bradley Pease, Shaun Bochow, Grace Sun

Submitter: Magdalena Antczak

DOI: 10.48546/workflowhub.workflow.1782.1

demux_bench
Stable

Portable genotype-free demultiplexing benchmarkign pipeline.

A portable pipeline for benchmarking genotype-free single-cell demultiplexing methods on simulated data.

The pipeline is designed to be generelisable to different datasets with arbitrary numbers of simulated mulitplexed samples. All software as part of pipeline is run through apptainer containers to ensure reproducibility and ease of use. The pipeline is designed to be run on a cluster with a slurm scheduler, but can be run locally ...

Type: Nextflow

Creators: Michael P Lynch, Leverages scripts developed by Weber et al (2021) DOI: https://doi.org/10.1093/gigascience/giab062

Submitter: Michael Lynch

DOI: 10.48546/workflowhub.workflow.1769.4

EC-Earth3 workflow without wrappers in MeluXina

EC-Earth3 workflow with wrappers running in MeluXina with Autosubmit 3, used to assess the effects of task aggregation on queueing times. Workflow configuration is based on the Auto-EC-Earth3's testing suite [1].

In order to reduce the size of the workflow, the /proj and /tmp directories have been deleted. Additionally, the experiment has been cleaned up with the Autosubmit cleanup command. Authorized users will be able to fetch the project files from the original remote source.

[1] Garcia Lopez, ...

Type: Autosubmit

Creators: Pablo Goitia, The Auto-EC-Earth team

Submitter: Pablo Goitia

EC-Earth3 workflow with wrappers in MeluXina

EC-Earth3 workflow with wrappers running in MeluXina with Autosubmit 3, used to assess the effects of task aggregation on queueing times. Workflow configuration is based on the Auto-EC-Earth3's testing suite [1].

In order to reduce the size of the workflow, the /proj and /tmp directories have been deleted. Additionally, the experiment has been cleaned up with the Autosubmit cleanup command. Authorized users will be able to fetch the project files from the original remote source.

[1] Garcia Lopez, ...

Type: Autosubmit

Creators: Pablo Goitia, The Auto-EC-Earth team

Submitter: Pablo Goitia

EC-Earth3 workflow without wrappers in MareNostrum 5

EC-Earth3 workflow with wrappers running in MareNostrum 5 with Autosubmit 3, used to assess the effects of task aggregation on queueing times. Workflow configuration is based on the Auto-EC-Earth3's testing suite [1].

In order to reduce the size of the workflow, the /proj and /tmp directories have been deleted. Additionally, the experiment has been cleaned up with the Autosubmit cleanup command. Authorized users will be able to fetch the project files from the original remote source.

[1] Garcia ...

Type: Autosubmit

Creators: Pablo Goitia, The Auto-EC-Earth team

Submitter: Pablo Goitia

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