Workflows

What is a Workflow?
738 Workflows visible to you, out of a total of 793
ERGA ONT+Illumina Assembly+QC Flye+HyPo v2403 (WF2)
Stable

The workflow takes raw ONT reads and trimmed Illumina WGS paired reads collections, and the estimated genome size and Max depth (both calculated from WF1) to run Flye and subsequently polish the assembly with HyPo. It produces collapsed assemblies (unpolished and polished) and runs all the QC analyses (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

score-assemblies
Stable

score-assemblies

A Snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina sequencing.

The workflow includes the following programs:

...

Type: Snakemake

Creator: Peter Menzel

Submitter: Peter Menzel

DOI: 10.48546/workflowhub.workflow.786.1

ont-assembly-snake
Stable

ont-assembly-snake

A Snakemake wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, and optionally Illumina data, using any combination of read filtering, assembly, long and short read polishing, and reference-based polishing.

Included programs

read filtering assembly long read polishing short read polishing reference-based polishing
Filtlong
...

Type: Snakemake

Creator: Peter Menzel

Submitter: Peter Menzel

DOI: 10.48546/workflowhub.workflow.787.1

Wound Healing Scrath Assay Image Analysis
Work-in-progress

This project is about the automated quantification of wound healing in high-throughput microscopy scratch assays.

Type: Galaxy

Creator: Christian Tischer

Submitter: Yi Sun

Lysozyme in water full version, using REMOTE dataset, two workers, data_persistence False

Lysozyme in water full COMPSs application run at MareNostrum IV, using full dataset with two workers

Type: COMPSs

Creator: Rosa M Badia

Submitter: Raül Sirvent

PyCOMPSs Probabilistic Tsunami Forecast (PTF) - Kos-Bodrum 2017 earthquake and tsunami test-case

PyCOMPSs implementation of Probabilistic Tsunami Forecast (PTF). PTF explicitly treats data- and forecast-uncertainties, enabling alert level definitions according to any predefined level of conservatism, which is connected to the average balance of missed-vs-false-alarms. Run of the Kos-Bodrum 2017 event test-case with 1000 scenarios, 8h tsunami simulation for each and forecast calculations for partial and full ensembles with focal mechanism and tsunami data updates.

Type: COMPSs

Creators: Louise Cordrie, Jorge Ejarque, Carlos Sánchez Linares, Jacopo Selva, Jorge Macías, Steven J. Gibbons, Fabrizio Bernardi, Roberto Tonini, Rosa M. Badia, Sonia Scardigno, Stefano Lorito, Finn Løvholt, Fabrizio Romano, Manuela Volpe, Alessandro D'Anca, Marc de la Asunción, Manuel J. Castro

Submitter: Jorge Ejarque

DOI: 10.48546/workflowhub.workflow.781.1

PyCOMPSs Probabilistic Tsunami Forecast (PTF) - Boumerdes-2003 earthquake and tsunami test-case

PyCOMPSs implementation of Probabilistic Tsunami Forecast (PTF). PTF explicitly treats data- and forecast-uncertainties, enabling alert level definitions according to any predefined level of conservatism, which is connected to the average balance of missed-vs-false-alarms. Run of the Boumerdes-2003 event test-case with 1000 scenarios, 8h tsunami simulation for each and forecast calculations for partial and full ensembles with focal mechanism and tsunami data updates.

Type: COMPSs

Creators: Louise Cordrie, Jorge Ejarque, Carlos Sánchez Linares, Jacopo Selva, Jorge Macías, Steven J. Gibbons, Fabrizio Bernardi, Roberto Tonini, Rosa M. Badia, Sonia Scardigno, Stefano Lorito, Finn Løvholt, Fabrizio Romano, Manuela Volpe, Alessandro D'Anca, Marc de la Asunción, Manuel J. Castro

Submitter: Jorge Ejarque

DOI: 10.48546/workflowhub.workflow.779.1

Jupyter Notebook Mutation Free Energy Calculations
Stable

Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)

Based on the official pmx tutorial.

This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial. ...

Type: Jupyter

Creators: Genís Bayarri, Adam Hospital

Submitters: Douglas Lowe, Genís Bayarri

DOI: 10.48546/workflowhub.workflow.55.6

Jupyter Notebook GMX Notebook Automatic Ligand Parameterization tutorial
Stable

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

OpenBabel and ACPype packages are used to **add hydrogens, energetically ...

Type: Jupyter

Creators: Genís Bayarri, Adam Hospital, Douglas Lowe

Submitters: Robin Long, Genís Bayarri

DOI: 10.48546/workflowhub.workflow.54.6

Galaxy Molecular Structure Checking
Stable

Molecular Structure Checking using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation. The workflow uses the BioExcel Building Blocks library (biobb). The particular structure used is the crystal structure of human Adenylate Kinase 1A (AK1A), in complex with the AP5A inhibitor (PDB code 1Z83).

**Structure ...

Type: Galaxy

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.778.1

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