Disclaimer

These extra exercises are open-ended, we don’t have any hints prepared but as always you can use Google, ChatGPT or ask teachers for assistance.

Author

These exercises where authored and tested by Kasper Thystrup Karstensen

Update finders_on_folder.sh

1. Using an example from Covid genome assembly advanced set up parameters -s (—sampledir), - and -o (—output) for the script.

2. Currently the output groups together different samples under a finder folder. Change that so output of all the finders is grouped under a sample folder.

3. Add a check that gives an error message if script doesn’t find any .fasta files in provided sample folder.

Update covid_assembly.sh

1. Using an example from pipeline development, set up a script that looks up all fastqs, and runs covid_assembly.sh on all the reads in the folder.

2. Create a step that concatenates all .fasta files into one file called sequences.fasta

3. Change nextclade to run on new sequences.fasta file instead of every single sample. Inspect output

If you finish everything and you are bored, ask Povilas for more extras :)