gffread | GTF utility providing format conversions , region filtering | Genomics library

I'm having issue getting my snakemake aggregate command to work. My hope is to take a given GTF file, look for separate regions within the GTF and if found write these regions to a separate file. Thus, I'm unsure the number of output GTF files each input GTF file will create. In order to solve this problem I'm attempting to use a snakemake checkpoint.

To do this I wrote a brief script called collapse_gtf_file.py which simply takes in a GTF file, and generates N number of files corresponding to the number of individual regions found. So if given the file test_regions.gtf which had three regions, it would generate test_regions_1.gtf, test_regions_2.gtf test_regions_3.gtf respectivly.

After said seperation, all GTF files should be converted to fasta files, and the aggregated.

However, I have not been able to get my checkpoint command to work. I can get the example cases to work, yet when I try and build a larger pipeline around this checkpoint it breaks.

So far I've tried following the checkpoint tutorial found here https://snakemake.readthedocs.io/en/stable/snakefile/rules.html#dynamic-files