Prodigal

Closes #33 (closed)

tools/cd-hit-est/example_usage/Snakefile

+configfile: "config.yaml"
+
+# ==== Snakefile path ====
+__cd-hit_rules = config.get("snakefiles", {}).get("cd_hit_est")
+
+__main_output_dir = config.get('output_dir', 'output')
+
+# ==== Main config ====
+SAMPLES = config.get('samples')
+__input_dir = config.get('input_dir', 'data')
+
+# ==== Run cd-hit ====
+__cd-hit_output_dir = f"{__main_output_dir}/cd-hit"
+__cd-hit_input = "{dir}/{{sample}}.fa".format(dir=__input_dir, sample="{sample}")
+__cd-hit_output = "{dir}/{{sample}}.fa".format(dir=__cd-hit_output_dir, sample="{sample}")
+include: __cd-hit_rules
+
+rule all:
+    input:
+        expand("{dir}/{{sample}}.fa".format(dir=__cd-hit_output_dir), sample=SAMPLES)