Refactor: Use only local files. Use chr19 in test_files.

Change config.yaml, prepare.smk, genome_process.sh and filter_anno_gtf.sh to use local files.
Add new annotation test files for chr19.
Change .md5 to these new outputs.

Closes #34

config/config.yaml

@@ -86,6 +86,7 @@ mir_list: ["miRNA", "miRNA_primary_transcript"]
 
 # Resources: miR annotations, chromosome name mappings
 # All of these are produced by the "prepare" workflow
-mirnas_anno: "results/homo_sapiens/chr19/mirna_filtered.bed"
+pre_mirnas_anno: "results/homo_sapiens/chr19/pre_mirna_filtered.bed"
+mirnas_anno: "results/homo_sapiens/chr19/mirna_mature_filtered.bed"
 isomirs_anno: "results/homo_sapiens/chr19/isomirs_annotation.bed"
 ...
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