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
- You do not need to edit and run setup.sh any more, this will be removed
- Edit config in
config.yaml - Edit config in
nextflow.config(scheduler, path to Wochenende, etc) - Get a small read fastq file as input (present in the repo for testing)
- Edit
start_nf.sh - Run
bash start_nf.sh
Output
- By default in output/wochenende
If missing or 0 sized bams in output
- Check most recent work folder
- cd work && ls -lrt
- Go into most recent folder and subfolder
- ls -l
- cat .command.err
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.