rbbt-util 5.28.2 → 5.28.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  data.tar.gz: f2a0e7c55aa053a7d559143b1ae235558355fd1f4f61f2845864e47b621e37fc
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+  metadata.gz: fd8348766af38ef48c379966ae2766e59fcb14714d78a5130856cdfef2d5a87eeabb4ae519a2fa6a2fa862d6b71cfff711eefe293b3f0954af6b0f70bbf58bdd
+  data.tar.gz: a8187db527df84d7db46e1cc049ed8e3a850188da16d0834408af102bf7f02977524786ab1267e6d047744d3e8cca3cc02c1382ede7b8766a61468867e2f8464

data/lib/rbbt/resource/path.rb

@@ -412,7 +412,9 @@ module Path
   end
 
   def replace_extension(new_extension = nil, multiple = false)
-    if multiple
+    if String === multiple
+      new_path = self.sub(/(\.[^\.\/]{1,5})(.#{multiple})?$/,'')
+    elsif multiple
       new_path = self.sub(/(\.[^\.\/]{1,5})+$/,'')
     else
       new_path = self.sub(/\.[^\.\/]{1,5}$/,'')

data/lib/rbbt/tsv/change_id.rb

@@ -58,13 +58,13 @@ module TSV
 
     identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
     identifiers = tsv.identifier_files.first if identifiers.nil?
-    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace and Organism.identifiers(tsv.namespace).exists?
+    identifiers = Organism.identifiers(tsv.namespace) if defined?(Organism) && identifiers.nil? && tsv.namespace && Organism.identifiers(tsv.namespace).exists?
     identifiers.namespace ||= tsv.namespace
 
     fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil 
     #index = identifiers.index :target => format, :fields => fields, :persist => persist_input, :order => true
 
-    grep = Organism.blacklist_genes(tsv.namespace).list  if identifiers.namespace and Organism.blacklist_genes(tsv.namespace).exists?
+    grep = Organism.blacklist_genes(tsv.namespace).list  if defined?(Organism) && identifiers.namespace && Organism.blacklist_genes(tsv.namespace).exists?
     if fields.nil?
       index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :persist => true, :order => true, :unnamed => true, :data_persist => true)
     else

data/lib/rbbt/tsv/util.rb

@@ -316,22 +316,30 @@ module TSV
 
   def to_single
     new = {}
-    case type
-    when :double
-      through do |k,v|
-        new[k] = v.first.first
-      end
-    when :flat
+
+    if block_given?
       through do |k,v|
-        new[k] = v.first
+        new[k] = yield v
       end
-    when :single
-      return self
-    when :list
-      through do |k,v|
-        new[k] = v.first
+    else
+      case type
+      when :double
+        through do |k,v|
+          new[k] = v.first.first
+        end
+      when :flat
+        through do |k,v|
+          new[k] = v.first
+        end
+      when :single
+        return self
+      when :list
+        through do |k,v|
+          new[k] = v.first
+        end
       end
     end
+
     self.annotate(new)
     new.type = :single
     new.fields = [new.fields.first] if new.fields.length > 1

data/lib/rbbt/workflow/integration/cromwell.rb

@@ -4,8 +4,13 @@ module Workflow
   Rbbt.claim Rbbt.software.opt.jar["wdltool.jar"], :url, "https://github.com/broadinstitute/wdltool/releases/download/0.14/wdltool-0.14.jar"
 
   def run_cromwell(file, work_dir, options = {})
+    cromwell_inputs_file = Misc.process_options options, :cromwell_inputs_file
     jar = Rbbt.software.opt.jar["cromwell.jar"].produce.find
-    CMD.cmd_log("java -jar '#{jar}' run '#{file}' --workflow-root='#{work_dir}'", options.merge("add_option_dashes" => true))
+    if cromwell_inputs_file
+      CMD.cmd_log("java -jar '#{jar}' run '#{file}' --workflow-root='#{work_dir}' -i #{cromwell_inputs_file}", options.merge("add_option_dashes" => true))
+    else
+      CMD.cmd_log("java -jar '#{jar}' run '#{file}' --workflow-root='#{work_dir}'", options.merge("add_option_dashes" => true))
+    end
   end
 
   def load_cromwell(file)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.28.2
+  version: 5.28.4
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-08-12 00:00:00.000000000 Z
+date: 2020-09-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake