Workflows

What is a Workflow?
1232 Workflows visible to you, out of a total of 1313
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 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 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 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

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

EC-Earth3 workflow with wrappers running in MareNostrum 4 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

EC-Earth3 workflow with wrappers running in MareNostrum 4 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

Generate annotated gb for fragments and add them to DB

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: Rebecca Bruni

Work-in-progress

This repository contains a Common Workflow Language (CWL) and Ro-Crate metadata definition for DTC-T1 workflow 6101, which is designed for providing tsunami impact forecasting following a tsunamigenic earthquake event, based on a probabilistic approach. The workflow integrates real-time earthquake data, runs HPC simulations, and generates tsunami hazard maps.

The main CWL implementation is found in WF6101.cwl, together with ST610106 and ST610109 describing complex steps. The file mini-ST610106.cwl ...

Type: Common Workflow Language

Creator: Marco Salvi

Submitters: Raül Sirvent, Pablo Orviz

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