Remove prepare_annotation directory. Rename process_data to snakemake.

.gitignore

prepare_annotation/.gitignore

prepare_annotation/Snakefile

prepare_annotation/cluster.json

prepare_annotation/config.yaml

prepare_annotation/other.fa

process_data/.gitignore

process_data/create_snakemake_flowchart.sh

process_data/run_snakefile.sh

scripts/fg_extract_transcripts.py

snakemake/Snakefile

snakemake/cluster.json

snakemake/config.yaml

snakemake/create_snakemake_flowchart.sh

snakemake/paired_end.snakemake

snakemake/preprocessing.snakefile

snakemake/run_snakefile.sh

snakemake/single_end.snakefile