Nextflow for reproducible and automated data analysis
21 and 22 November 2024
General context
You will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language.
- Understand Nextflow's basic concepts: channels, processes, modules, workflows, etc.
- Write and run a Nextflow pipeline
- Write and modify config files for storing parameters related to computing hardware as well as pipeline dependent parameters
Bioinformaticians with no or little knowledge of containers or workflow pipelines.
You're familiar with doing bioinformatics on the command-line and with Docker.
- If you have no experience with command line we strongly recommend to follow the Linux initiation training first.
- If you have no experience with Docker you can follow the Docker training.
Trainers
Kobe Lavaerts
Bioinformatician at VIB Nucleomics Core in Leuven. Currently mainly focusing on operating and developing routine pipelines for processing raw sequencing data.
Nicolas Vannieuwkerke
Nicolas Vannieuwkerke is a bioinformatician at CMGG (UZ Ghent) who mainly focuses on developing and maintaining Nextflow pipelines for the diagnostic NGS analyses. He is a very active member of the Nextflow community as a Nextflow ambassador and is part of the nf-core core team. Nf-core is the largest Nextflow community that creates and maintains a number of best-practice pipelines and developer resources.
Program
09:30 - 10:30 - Building Blocks
10:30 - 10:45 - Break
10:45 - 12:00 - Processes and Workflows
12:00 - 13:00 - Lunch
13:00 - 14:45 - Creating our first pipeline
14:45 - 15:00 - Break
15:00 - 17:30 - Modules and Subworkflow
09:30 - 10:45 - Config files, Containers and Reports
10:45 - 11:00 - Break
11:00 - 12:30 - Exercise
12:30 - 13:30 - Lunch
13:45 - 15:00 - Project Challenge
15:00 - 15:15 - Break
15:15 - 17:00 - Project Challenge
Practical info
21 November 2024 - 22 November 2024
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
21 November 2024 - 22 November 2024
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
21 November 2024 - 22 November 2024
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
21 November 2024 - 22 November 2024
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.
21 November 2024 - 22 November 2024
Leuven - Campus Gasthuisberg
Room: R.CBD.ON5-5thFloor-404-28.05.347