sushi_fabric 0.9.3 → 0.9.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 84de00c578f9193950709558ab94634ef637a12e
-  data.tar.gz: fb3af7878169c568fdcf8d291dcc354ef3fa5142
+  metadata.gz: 8d9c4e224a34d7d928e2a656e07e41a943a8793c
+  data.tar.gz: b5f78a77a230d72f6ca9825d5d77b3a4a4df90b1
 SHA512:
-  metadata.gz: 7e83696b93bbc02318541f5e7be8fe406d86ab2330fc28b2a1ec3b256a568bff3b4e3771b925a83adceec0c6984ff0f842d4a924f94b52ee46b4c34aec558128
-  data.tar.gz: 32e32f6a899a3e1d435da76c945a3c76835ff8cc0fb02b8b484fc36333dc5b03b02be9a5f7f14cfaaba56fcab1e58e638fa2e2478f036c685fed9b456cbf6195
+  metadata.gz: 926b9b3975f334ffe5203985cee62659e5d9280da0278e2c67c64e6beb96dfe3e8579ae4fc8665bc1276d2203cf3e36f8a46966710ef875756bbf91a1a9f8f05
+  data.tar.gz: 3f85a0c2ef2a2a63d0a87c4ecd09aa2c99952298cab670444a73111cfc0960ecbd08ce7ea0792e9d20d200f4e79b8acda05fccaeb71ce310da3eed2314742a54

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20191114-151205'
+# Version = '20191115-103323'
 
 require 'csv'
 require 'fileutils'
@@ -243,6 +243,7 @@ class SushiApp
     @module_source = MODULE_SOURCE
     @modules = []
     #@workflow_manager = workflow_manager_instance||DRbObject.new_with_uri(WORKFLOW_MANAGER)
+    @last_job = true
   end
   def set_input_dataset
     if @dataset_tsv_file
@@ -429,6 +430,7 @@ umask 0002
 SCRATCH_DIR=#{@scratch_dir}
 GSTORE_DIR=#{@gstore_dir}
 INPUT_DATASET=#{@input_dataset_tsv_path}
+LAST_JOB=#{@last_job.to_s.upcase}
 echo "Job runs on `hostname`"
 echo "at $SCRATCH_DIR"
 mkdir $SCRATCH_DIR || exit 1
@@ -631,36 +633,22 @@ rm -rf #{@scratch_dir} || exit 1
     @out.close
   end
   def sample_mode
-    set_job_script =-> (dataset_) do
-        @dataset = dataset_
+    selected_samples = Hash[*@params['samples'].split(',').map{|sample_name| [sample_name, true]}.flatten]
+    @dataset_hash.each_with_index do |row, i|
+      @dataset = Hash[*row.map{|key,value| [key.gsub(/\[.+\]/,'').strip, value]}.flatten]
+      if selected_samples[@dataset['Name']]
         sample_name = @dataset['Name']||@dataset.first
         @job_script = if @dataset_sushi_id and dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
                         File.join(@job_script_dir, @analysis_category + '_' + sample_name) + '_' + dataset.name.gsub(/\s+/,'_') + '.sh'
                       else
                         File.join(@job_script_dir, @analysis_category + '_' + sample_name) + '.sh'
                       end
+        @last_job = (i == @dataset_hash.length - 1)
         make_job_script
         @job_scripts << @job_script
         @result_dataset << next_dataset
-    end
-    selected_samples = Hash[*@params['samples'].split(',').map{|sample_name| [sample_name, true]}.flatten]
-    last_sample = nil
-    @dataset_hash.each do |row|
-      @dataset = Hash[*row.map{|key,value| [key.gsub(/\[.+\]/,'').strip, value]}.flatten]
-      if selected_samples[@dataset['Name']]
-        header = if header_ = row.keys.find{|h| h.tag?('Last')}
-                   header_.gsub(/\[.+\]/,'').strip
-                 end
-        if header and eval(@dataset[header])
-          last_sample = @dataset
-        else
-          set_job_script.(@dataset)
-        end
       end
     end
-    if last_sample
-      set_job_script.(last_sample)
-    end
   end
   def dataset_mode
     selected_samples = Hash[*@params['samples'].split(',').map{|sample_name| [sample_name, true]}.flatten]

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "0.9.3"
+  VERSION = "0.9.4"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.9.3
+  version: 0.9.4
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-11-14 00:00:00.000000000 Z
+date: 2019-11-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler