Workflows

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69 Workflows visible to you, out of a total of 79

Workflow for sequencing with ONT nanopore, from basecalling to assembly quality. Steps:

  • Guppy (basecalling of raw reads)
  • MinIONQC (quality check)
  • FASTQ merging from multi into one file
  • Kraken2 (taxonomic classification)
  • Krona (classification visualization)
  • Flye (de novo assembly)
  • Medaka (assembly polishing)
  • QUAST (assembly quality reports)

The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous) or by using the conda / pip environments as shown ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Jasper Koehorst

Work-in-progress

Abstract CWL Automatically generated from the Galaxy workflow file: GTN 'Pangeo 101 for everyone - Introduction to Xarray'.

In this tutorial, we analyze particle matter < 2.5 μm/m3 data from Copernicus Atmosphere Monitoring Service to understand Xarray Galaxy Tools:

  • Understand how an Xarray dataset is organized;
  • Get metadata from Xarray dataset such as variable names, units, coordinates (latitude, longitude, level), etc;
  • Plot an Xarray dataset on a geographical map and learn to customize ...

Type: Galaxy

Creators: None

Submitter: Anne Fouilloux

Stable

This workflow extracts 5 different time periods e.g. January- June 2019, 2020 and 2021, July-December 2019 and 2020 over a single selected location. Then statistics (mean, minimum, maximum) are computed. The final products are maximum, minimum and mean.

Type: Galaxy

Creators: None

Submitter: Anne Fouilloux

DOI: 10.48546/workflowhub.workflow.251.1

Stable

Description

The workflow takes an input file with Cancer Driver Genes predictions (i.e. the results provided by a participant), computes a set of metrics, and compares them against the data currently stored in OpenEBench within the TCGA community. Two assessment metrics are provided for that predictions. Also, some plots (which are optional) that allow to visualize the performance of the tool are generated. The workflow consists in three standard steps, defined by OpenEBench. The tools needed ...

Type: Nextflow

Creators: José Mª Fernández, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas

Submitter: Laura Rodriguez-Navas

Stable

Summary

This notebook shows how to integrate genomic and image data resources. This notebook looks at the question Which diabetes related genes are expressed in the pancreas?

Steps:

  • Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the genes.
  • Using the list of found genes, search in the Image Data Resource (IDR) for images linked to the genes, tissue and disease.

We use the intermine API and the IDR API

The notebook can be launched ...

Work-in-progress

atavide is a complete workflow for metagenomics data analysis, including QC/QA, optional host removal, assembly and cross-assembly, and individual read based annotations. We have also built in some advanced analytics including tools to assign annotations from reads to contigs, and to generate metagenome-assembled genomes in several different ways, giving you the power to explore your data!

atavide is 100% snakemake and conda, so you only need to install the snakemake workflow, and then ...

Type: Snakemake

Creators: None

Submitter: Rob Edwards

DOI: 10.48546/workflowhub.workflow.241.1

Stable

Exome SAMtools Workflow

Type: Nextflow

Creator: Laura Rodriguez-Navas

Submitter: Laura Rodriguez-Navas

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