coutinho_assembly 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 6c3a4566c5537b5251e65b845635cbce66f74668
+  metadata.gz: 9cef186eff0a2e1a788f727e0c4f78aac4399a9a
+  data.tar.gz: 39ad07d3c8328f142070dfd24f5ff48a2b9cd8cc
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    coutinho_assembly (0.1.0)
+    coutinho_assembly (0.2.0)
 
 GEM
   remote: https://rubygems.org/

data/README.md

@@ -22,7 +22,11 @@ Or install it yourself as:
 
 ## Usage
 
-TODO: Write usage instructions here
+For usage instructions type
+
+```
+coutinho_assembly --help
+```
 
 ## Development
 

data/exe/coutinho_assembly

@@ -77,6 +77,11 @@ opts = Optimist.options do
       "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",
@@ -138,6 +143,11 @@ Rya::AbortIf.abort_if num_threads < 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]

data/lib/coutinho_assembly/version.rb

@@ -1,5 +1,5 @@
 module CoutinhoAssembly
-  VERSION = "0.1.0"
+  VERSION = "0.2.0"
 
   COPYRIGHT = "2019 Ryan Moore"
   CONTACT   = "moorer@udel.edu"

data/lib/coutinho_assembly.rb

@@ -58,6 +58,8 @@ module CoutinhoAssembly
 
         if preset == "meta-sensitive"
           cmd += " --presets meta-sensitive"
+        elsif preset == "meta-large"
+          cmd += " --presets meta-large"
         elsif preset == "fast"
           cmd += " --k-list 21"
         end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: coutinho_assembly
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-01-13 00:00:00.000000000 Z
+date: 2019-04-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler