feat: merge updated workflow with miR processing

.gitignore

README.md

RUNS/JOB/prepare_annotation/cluster.json

RUNS/JOB/prepare_annotation/config.yaml

RUNS/JOB/prepare_annotation/run_workflow_slurm.sh

environment.root.yml

environment.yml

images/rule_graph_prepare_annotation.svg

images/workflow_dag_prepare_annotation.svg

scripts/filter_anno_gtf.sh

scripts/filter_mir_1_anno.sh

scripts/genome_process.sh

scripts/map_chromosomes.pl

scripts/validation_fasta.py

test/cluster_prepare_annotation.jsob

test/config_prepare_annotation.yaml

test/expected_output.files

test/expected_output.md5

test/test_workflow_slurm.sh

workflow/prepare_annotation/Snakefile