See documentation on our Wiki at https://github.com/MHH-RCUG/nf_wochenende/wiki
This is a more portable version of the alignment pipeline Wochenende which uses Nextflow. This should allow other users to start Wochenende more easily and efficiently.
- Colin Davenport
- Lisa Hollstein
Work in progress (Spring-Summer 2022).
Running nf_wochenende
- Edit config in
config.yaml - Edit config in
nextflow.config(scheduler, etc) - Get a small read fastq file as input
- Edit
start_nf.sh - Run
bash start_nf.sh
Not touched to date
- shell scripts, wochenende_postprocess etc
- tidy all scripts to subdirs
Note that that only process used in the run_nf_wochenende.nf file is wochenende (see the workflow section). Other processes might be needed later, or may be removed.