I am noticing in the Genomics Course under 0.2.3. Repeat the process on the other two samples there is a note that says “Once this completes, you should have three files ending in .g.vcf in your work directory (one per sample) and their respective index files ending in .g.vcf.idx.”
I understand that this means to find the files within the results_genomics/ folder in the course work directory. I am wondering though if the use of work directory may be confusing to someone less familiar with Nextflow, knowing that one of the native output folders of the Nextflow pipeline is called “work” and that this folder will be in the work directory referenced since a pipeline was run in the first genomics session. I am wondering if this might want to be clarified, in case someone might be looking for these results in that Nextflow work folder mistakenly? Feel free to disregard this if you feel that it is not confusing, but I just wanted to bring it up in case.
In command line lingo, the “work directory” or current working directory, is the folder in a computer’s file system where a program is currently operating and where commands are executed. The `gatk` command you’re running will generate the files in your current work directory (where you are running this command from).
Apart from that, I agree with you, as in the Nextflow context we’re usually referring to something else when mentioning work directory. I will open a PR to improve clarity on this. Thanks for the feedback!
I completely get it—and personally I didn’t find it too confusing. One of my students actually pointed out the confusion, and I wanted to make sure to bring it up since it was a good perspective!