Reproducible genomics workflows using Nextflow and nf-core

Repository for the BovReg Nextflow workshop organized by the CRG on 17-20 November 2020.

Programme

The workshop will include a Nextflow training and hackathon, Keynote speakers, and contributed talks selected from participants abstracts. The preliminary event schedule can be found here.

Format

Online workshop.

Interesting links

• Live streams on BovReg YouTube Channel
• Use the BovReg Slack organization for discussion and collaboration.
• Follow us on Twitter and stay tunned during the event and beyond.

Note: If you are a registered participant you should have received the corresponding Zoom links for the different sessions where you have been accepted.

Talks

Talks will be streamed on Zoom for registered participants and in Youtube for any other person interested. Questions can be posted on Zoom or in the dedicated Slack channel #workshop-nov-2020-talks.

• Introduction to Nextflow

  Evan Floden - Nextflow developer and CEO & Co-founder of Seqera Labs, Spain.

  Watch it here.

• Introduction to nf-core

  Phil Ewels - nf-core core team, Head of Genomics Applications Development at SciLifeLab, Sweden.

  Watch it here.

• Running nf-core pipelines + Contributing to nf-core (tutorial)

  Phil Ewels - nf-core core team, Head of Genomics Applications Development at SciLifeLab, Sweden.

  Watch it here.

• Featured nf-core pipelines

  Harshil Patel - nf-core core team, Senior Bioinformatician of the Bioinformatics and Biostatistics Facility at the Francis Crick Institute, UK.

  Watch it here.

• Master of Pores: "A nanopore processing pipeline"

  Luca Cozzuto - NGS data analysis Coordinator of CRG Bioinformatics Core at the Centre for Genomic Regulation, Spain.

  Watch it here.

• Introduction to DSL2

  Paolo di Tommaso - Creator and project leader of Nextflow and CTO & Co-founder of Seqera Labs, Barcelona, Spain.

  Watch it here.

Flash talks selected from participants abstracts

Talks will be streamed on Zooom for registered participants and in Youtube for the general public. Questions can be posted on Zoom, Youtube comments or in the dedicated Slack channel #workshop-nov-2020-flash-talks.

Find the presentation abstracts at this link.

Find all the flash talk sessions recorded on the following links:

• Day 1
• Day 2
• Day 3
• Day 4

Nextflow training

Note: Nextflow training places are limited. Only participants that received the confirmation email can attend.

Nextflow training will take place during mornings. If you have been accepted in the training session, you should have received the information of how to attend before the first session.

The slack channel for the training is #workshop-nov-2020-training.

Hackathon projects:

The hackathon is free and open to everybody. However, to help us organize the event we ask you to register here. Note, that in case you are interested you can propose your own hackathon project. This will require that you lead the project and pitch one slide during the hackathon introduction session (Tuesday, 14:30-15:00) explaining which is the objective/idea of your project. You can use the same registration form to provide us with this information. In any case, there are already several projects proposed by registered participants. Take a look at the Hackathon projects section here to see the already proposed ideas.

We would like the hacakthon to be dynamic and self-organized so feel free to work in more than one project and do not restrict to your first option. The selected hackathon projects have its own Slack channel allowing all the project participants to communicate. Also, we propose that the different projects make a presentation of the advances achieved on the previous day using HackMD slides (see below) at the starting of each day hackathon session.

Project 1 - From Snakemake to Nextflow

• Slack channel: #hackathon-nov-2020-pr1-snakemake-nextflow
• Slides on HackMD: Edit, view
• Link to the fork of the GitHub project repository on BovReg

Project 2: WGS data analysis pipeline

• Slack channel: #hackathon-nov-2020-pr2-wgs-pipeline
• Slides on HackMD: Edit, view
• Link to the fork of the GitHub project repository on BovReg

Project 4: RNA-seq analysis pipeline

• Slack channel: #hackathon-nov-2020-pr4-rnaseq-pipeline
• Slides on HackMD: Edit, view
• Link to the fork of the GitHub project repository on BovReg

Project 7: Bacterial DNA analysis pipeline

• Slack channel: #hackathon-nov-2020-pr7-bacterial-dna-pipeline
• Slides on HackMD: Edit, view
• Link to the fork of the GitHub project repository on BovReg

Poster

Funding

BovReg project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement ID. 815668.