Configuration Parameters¶
Edit config.yaml with the following keys:
| Key | Description | Example |
|---|---|---|
read |
Glob pattern for input reads | data/reads/illumina_reads_*.fasta.gz |
reference |
Reference genome FASTA | data/ref/hg38_partial.fasta.gz |
annotations |
Directory containing annotation files | data/annotations |
scripts_dir |
Directory containing the Perl scripts | scripts |
results_dir |
Output directory for pipeline results | results |
Example config.yaml:
read: "data/reads/illumina_reads_*.fasta.gz"
reference: "data/ref/hg38_partial.fasta.gz"
annotations: "data/annotations"
scripts_dir: "scripts"
results_dir: "results"