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Scientific topics: Workflows 

Introduction to Workflows with Common Workflow Language

Introduction to workflow thinking for novices, using the Common Workflow Language

Scientific topics: Workflows

Operations: RNA-Seq analysis

Keywords: cwl, commonwl, sciworkflows, workflows

Resource type: Carpentries style curriculum

Introduction to Workflows with Common Workflow Language http://tess.elixir-uk.org/materials/introduction-to-workflows-with-common-workflow-language Introduction to workflow thinking for novices, using the Common Workflow Language Stian Soiland-Reyes Toby Hodges Sehrish Kanwal Pedro L Fernandes Workflows cwl, commonwl, sciworkflows, workflows esearchers and research software engineers who would like to begin automating their analyses in workflows.
Tutorial on developing Building Blocks

This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them.

Scientific topics: Personalised medicine, Workflows, Bioinformatics

Keywords: HPC, building blocks

Resource type: Tutorial

Tutorial on developing Building Blocks http://tess.elixir-uk.org/materials/tutorial-on-developing-building-blocks This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them. Personalised medicine Workflows Bioinformatics HPC, building blocks Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities
Introduction to Nextflow workshop

workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available...

Scientific topics: Workflows

Keywords: Nextflow, DSL2

Resource type: Presentation, course materials

Introduction to Nextflow workshop http://tess.elixir-uk.org/materials/introduction-to-nextflow-workshop workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available [here](https://github.com/vibbits/nextflow-jnj/blob/master/presentation/slidedeck.pdf) Workflows Nextflow, DSL2 bioinformaticians
How to use V-pipe (SARS-CoV-2 data)

How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data)

Scientific topics: Workflows, Genetic variation, Virology

Operations: Read pre-processing, Alignment, Variant calling

Keywords: coronavirus, NGS bioinformatics, Variant-calling

Resource type: Computer Software, workflow

How to use V-pipe (SARS-CoV-2 data) http://tess.elixir-uk.org/materials/how-to-use-v-pipe-sars-cov-2-data How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data) Workflows Genetic variation Virology coronavirus, NGS bioinformatics, Variant-calling bioinformaticians Biologists, Genomicists, Computer Scientists
How to use Common Workflow Language

**This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).**

Scientific topics: Workflows

Keywords: commonwl, common workflow language, CWL, Workflows, eLearning, EeLP

Resource type: Installation instructions, Manual

How to use Common Workflow Language http://tess.elixir-uk.org/materials/how-to-use-common-workflow-language **This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).** Rob Finn Michael Crusoe Workflows commonwl, common workflow language, CWL, Workflows, eLearning, EeLP bioinformaticians life scientists programmers
Galaxy for NGS analysis: A web-based platform for data intensive biological research

Galaxy is an open, web-based platform for data intensive biomedical research. It offers an accessible, reproducible and transparent computational workbench for the biologist. This workbench is very useful in automating repeated analysis steps in the form of workflows. The workbench interface is...

Scientific topics: Workflows, High-throughput sequencing, Nucleic acid sequence analysis, Bioinformatics

Keywords: John Innes Centre, JIC

Galaxy for NGS analysis: A web-based platform for data intensive biological research http://tess.elixir-uk.org/materials/galaxy-for-ngs-analysis Galaxy is an open, web-based platform for data intensive biomedical research. It offers an accessible, reproducible and transparent computational workbench for the biologist. This workbench is very useful in automating repeated analysis steps in the form of workflows. The workbench interface is simple and intuitive, supports collaboration and integrates data and analysis tools together in a single place. Workflows High-throughput sequencing Nucleic acid sequence analysis Bioinformatics John Innes Centre, JIC
Galaxy workflows

This workshop/tutorial will familiarise you with the Galaxy workflow engine. It will cover the following topics: Logging in to the server How to construct and use a workflow by various methods How to share a workflow

Scientific topics: Workflows

Keywords: bioinformatics

Galaxy workflows http://tess.elixir-uk.org/materials/galaxy-workflows This workshop/tutorial will familiarise you with the Galaxy workflow engine. It will cover the following topics: Logging in to the server How to construct and use a workflow by various methods How to share a workflow Vicky Schneider Workflows bioinformatics Biologists
Introduction to the analysis of NGS data

This training is a prerequisite introduction to a series of trainings on the analysis of NGS data for different applications: 'Hands-on introduction to NGS variant analysis', 'RNA-Seq analysis for differential expression', and 'Hands-on introduction to ChIP-Seq analysis'. If you want to follow...

Scientific topics: Workflows, Sequence assembly

Introduction to the analysis of NGS data http://tess.elixir-uk.org/materials/introduction-to-the-analysis-of-ngs-data This training is a prerequisite introduction to a series of trainings on the analysis of NGS data for different applications: 'Hands-on introduction to NGS variant analysis', 'RNA-Seq analysis for differential expression', and 'Hands-on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings, you have to follow this introduction. The training will give you all the background that you will need in the later NGS trainings. Workflows Sequence assembly Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09