jelmerp
commented
4 months ago Presentation
| Aspect | Max. points | Your points |
|---|---|---|
| Technical content | 3 | 3 |
| Contextualization | 3 | 3 |
| Delivery | 3 | 3 |
| Clarity | 3 | 2 |
| Questions for others | 3 | 1 |
| total | 15 | 12 |
Great presentation! A couple more questions for others would have been nice.
Final submission
| Aspect | Max. points | Your points | Comment |
|---|---|---|---|
| Project organization | 4 | 3 | |
| Project background and documentation | 4 | 4 | Excellent! |
| Good practices in scripts | 4 | 2 | |
| Workflow reproducibility | 4 | 3 | |
| Slurm jobs at OSC | 3 | 2 | |
| Project/coding quality | 3 | 3 | |
| Version control | 3 | 2 | Too bad about the problem with the initial repo. |
| total | 25 | 19 |
Comments:
-
Project organization:
- Some files are missing, like your concatenated FASTQ files.
- It would have been good to move the modified config file out of the MetONTIIME pipeline. You put that pipeline appropriately in a folder
programs, but a modified config file would be better off with your runner script or in the metadata.
-
Good practices in scripts:
- Your scripts don't take arguments, and...
- ...you are hardcoding the absolute/full path to your
BASE_DIRin your primary scripts - Reporting is minimal, no
dateor "Starting script" or "Done with script" etc.
-
Slurm jobs:
- Your main Nextflow script doesn't need 16 cores, just 1. It will be submitting jobs itself.
-
Miscellaneous:
- You have
# workDir="/fs/ess/PAS2700/users/meyer1556/Final_Project/raw_data/concatenated_fastq_gz", but the Nextflow workdir isn't the dir where the data is, but where the jobs/processes are run and the initial results go. This should ideally be a dir in/fs/scratch. All of that was discussed in week 6 when we ran the nf-core rnaseq pipeline.
- You have
Hey, @jelmerp! Sorry for being a bit late. I was thrown off by having to create a new repository due to issues with pushing to the last one.