coutinho_assembly in coutinho_assembly-0.2.0

- old
+ new

@@ -75,10 +75,15 @@
       default: 1)
   opt(:max_attempts,
       "Max no. retries before giving up on a pipeline step.",
       default: 10)
 
+  # Megahit options
+  opt(:megahit_presets,
+      "meta-sensitive, meta-large, or fast",
+      default: "meta-sensitive")
+
   # External programs I depend on
   opt(:megahit_binary,
       "Path to megahit binary",
       default: "~/bin/megahit")
   opt(:sample_seqs_binary,
@@ -135,9 +140,14 @@
 
 Rya::AbortIf.abort_if num_threads < 1,
                       "--num-threads must be at least 1"
 Rya::AbortIf.abort_if max_attempts < 1,
                       "--max-attempts must be at least 1"
+
+GOOD_PRESETS = %w[meta-sensitive meta-large fast]
+megahit_preset = opts[:megahit_presets]
+Rya::AbortIf.abort_unless megahit_preset.nil? || GOOD_PRESETS.include?(megahit_preset),
+                          "--megahit-presets must be one of #{GOOD_PRESETS.join(", ")}.  Got #{megahit_preset}"
 
 megahit_binary     = opts[:megahit_binary]
 sample_seqs_binary = opts[:sample_seqs_binary]
 zip_binary         = opts[:zip_binary]
 