Refactor code to use only local files. Create new test files using chr19.

RUNS/JOB/map/intermediate_files.txt

config/config.yaml

config/config_template.yaml

scripts/filter_anno_gtf.sh

scripts/genome_process.sh

test/config.yaml

test/expected_output.md5

test/test_cleanup.sh

...st_files/homo_sapiens/chr19/GRCh38_UCSC2ensembl_chr19.txt

...es/homo_sapiens/chr19/Homo_sapiens.GRCh38.98.chr19.gtf.gz

...sapiens/chr19/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz

test/test_files/homo_sapiens/chr19/hsa_chr19.gff3

workflow/config.yaml

workflow/rules/prepare.smk