Project Submission

[awiedemer]

@jelmerp

See README.md for submission notes.

runner_script.sh contains information about how to run each script. Each script is annotated more in detail with what is actually happening.

[jelmerp]

Aspect	Max. points	Your points
Technical content	3	3
Contextualization	3	3
Delivery	3	3
Clarity	3	3
Questions for others	3	1
Tuesday lunch special		1
total	15	14

Great presentation! Only some more questions for others would have been nice.

Final submission

Aspect	Max. points	Your points	Comment
Project organization	4	2	Somewhat disorganized with e.g. many Slurm files and some dumped cores right in the project root dir, and no single results dir.
Project background and documentation	4	4
Good practices in scripts	4	2	See below.
Workflow reproducibility	4	2	See below.
Slurm jobs at OSC	3	3
Project/coding quality	3	3
Version control	3	3	Great job with granular commits!
total	25	19

Nice job! Just a somewhat mixed bag on the best practices and reproducibility fronts, with some really great commenting and reporting, for example, but also weaknesses:

• It would have been better to also have a script for FastQC just like you have a script for Kraken and Bracken, instead of running FastQC directly in the runner script.

• It would have been better to use loops in your runner script instead of inside run_bracken.sh and run_kracken2.sh.

• You should avoid having absolute paths in the primary scripts, like /fs/ess/PAS2700/users/$USER/class_project/ in setup_kraken2_databases.sh. These only need to be in the runner script.

• You have sbatch scripts/setup_kraken2_databases "$K2DB" but the script has the extension .sh, so this failed for me.

• What is going on in line 72 of your runner script? This isn't valid code. I guess the 35 75 was accidentally pasted in there?

  K2DB=35 75/fs/ess/PAS2700/users/awiedemer673/class_project/kraken2/database

• Minor, but set -euo pipefail is actually not appropriate in the runner script, this is meant for scripts that are run non-interactively.