jelmerp
commented
3 years ago | Aspect | Max. points | Your points | |
|---|---|---|---|
| Scripts | 4 | 3.5 | More extensive annotation (commenting) of scripts is needed. |
| Overview of scripts | 3 | 2 | From the overview, it is not really clear how many scripts there will be an what each script's function will be.[1] |
| To-do list | 1.5 | 1 | You didn't mention how you aim to tie things together, e.g. with a bash script or Snakemake. |
| Git commits | 1.5 | 1.5 | |
| TOTAL | 10 | 8 |
[1] Also, in the scripts dir, you have two pairs of scripts, but I did not see an explanation of how these fit together. Even with some simple script numbering or more consistent naming this could have been made fairly clear at a glance, but now, one has to carefully look at the contents of the scripts to see that fastq_file_list.sh goes with renaming.sh, and that gzip_file_list.sh goes with unzip.sh.
Some other remarks:
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I haven't looked at the code of the renaming script(s) in too much detail, because the shell script is best worked-out, but I think you are aiming to do it with Python now (but that script is still in the sandbox dir and completely unannotated). If you would like some feedback on the contents of your scripts when they are further worked-out prior to your final submission, you can always open a new Issue, and I would be happy to look at it.
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Both of your "main"/"worker" scripts,
renaming.shandunzip.sh, loop over a list of files. I think it is generally better to have such scripts process one file only, certainly for the more complex renaming case (and I know you will discard the unzipping script). Then, another script, along the lines of thefastq_file_list.shscript, could do the looping -- or you could let Snakemake take care of this.
Hi @jelmerp The overview and to-do list are in the same markdown file titled OverviewREADME. All of my scripts are in the scripts folder, with the python scripts still in the sandbox folder as I was testing them. Please let me know if there are any other things you think I could improve upon.