rbbt-util 5.33.2 → 5.33.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 8580df0b38d805739fe3ad80e688c92a5c31305893ef1cf6cfccd88c0aaccc7a
+  metadata.gz: 3ffb05883cf1e7eda628395b50967322b42240ace100fb73a2f4c4a1ed5e8d27
+  data.tar.gz: 8b25c002f68b88dc0ba1f09c041258ee0ca15d4fc6f8dc3df5de37ea2473d059
 SHA512:
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+  metadata.gz: 7b74e527336830eecb1cad52bb13cbcb335c734a18e9261d87cfba6da93422cf94a826e97d43c6ef1d37d122623408230d80a037a9a91000fa95a6cf9c818cf6
+  data.tar.gz: 8b8de5c12aac8dfae5f68018cb5aae4023b78993fa78aa7cf93cacc16eea4c2b959f75190ead6862502ecc75ae3ccd9cc462b1db26930943447a758f1f359cd9

data/lib/rbbt/hpc/orchestrate/batches.rb

@@ -11,7 +11,7 @@ module HPC
         iii :END_BATCHES
       else
         n = batch.dup
-        n[:deps] = n[:deps].collect{|b| b[:top_level] }
+        n[:deps] = n[:deps].collect{|b| b[:top_level] } if n[:deps]
         iif n
       end
     end
@@ -79,14 +79,14 @@ module HPC
 
       batches.each do |batch|
         jobs = batch[:jobs]
-        all_deps = jobs.collect{|d| job_dependencies(d) }.flatten.uniq
+        all_deps = jobs.collect{|d| job_dependencies(d) }.flatten.uniq - jobs
 
         minimum = all_deps
         all_deps.each do |dep|
           minimum -= job_dependencies(dep)
         end
 
-        all_deps = minimum
+        all_deps = minimum 
         deps = all_deps.collect do |d|
           (batches - [batch]).select{|batch| batch[:jobs].collect(&:path).include? d.path }
         end.flatten.uniq

data/lib/rbbt/util/cmd.rb

@@ -75,7 +75,7 @@ module CMD
 
     string = ""
     options.each do |option, value|
-      raise "Invalid option key: #{option.inspect}" if option.to_s !~ /^[a-z_0-9\-=]+$/i
+      raise "Invalid option key: #{option.inspect}" if option.to_s !~ /^[a-z_0-9\-=.]+$/i
       #raise "Invalid option value: #{value.inspect}" if value.to_s.include? "'"
       value = value.gsub("'","\\'") if value.to_s.include? "'"
 

data/lib/rbbt/workflow/definition.rb

@@ -92,7 +92,12 @@ module Workflow
         self.dependencies = self.dependencies - [dep]
         Open.rm_rf self.files_dir if Open.exist? self.files_dir
         FileUtils.cp_r dep.files_dir, self.files_dir if Open.exist?(dep.files_dir)
-        Open.ln_h dep.path, self.tmp_path
+
+        if dep.overriden
+          Open.link dep.path, self.tmp_path
+        else
+          Open.ln_h dep.path, self.tmp_path
+        end
 
         case remove.to_s
         when 'true'

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

@@ -4,7 +4,7 @@ module Workflow
   end
 
   def self.nextflow_includes(file)
-    Open.read(file).scan(/^include\s*{\s*(.*?)(?:\s*as.*?)?}\s*from\s+"(.*?)"(?:\s*params.*)?/).collect{|p| p}.uniq
+    Open.read(file).scan(/^include\s*{\s*([^\s]*?)\s+.*?}\s*from\s+["'](.*?)["'](?:\s*params.*)?/).collect{|p| p}.uniq
   end
 
   def self.nextflow_recursive_params(file)
@@ -48,25 +48,43 @@ module Workflow
     task name => result do 
       work = file('work')
       profile = config :profile, :nextflow
+      config_file = config :config, :nextflow
 
-      new_inputs = inputs.zip(inputs.fields).collect do |v,f|
-        if String === v && m = v.match(/^JOB_FILE:(.*)/)
-          file(m[1]) 
-        elsif v.nil?
-          Rbbt::Config.get(['nextflow', f] * "_", 'default', f)
+      nextflow_inputs = {}
+
+      inputs.zip(inputs.fields).collect do |v,f|
+        v = if String === v && m = v.match(/^JOB_FILE:(.*)/)
+              file(m[1]) 
+            elsif v.nil?
+              Rbbt::Config.get(['nextflow', f] * "_", 'default', f)
+            else
+              v
+            end
+
+        if f.to_s.include?("-") 
+          p,_sep, section = f.to_s.partition("-")
+          name = [section, p] * "."
         else
-          v
+          name = f
         end
+          
+        nextflow_inputs[name] = v
       end
       
-      inputs.replace new_inputs
-
       Misc.in_dir file('stage') do
-        if profile
-          cmd("nextflow run -work-dir #{work} -ansi-log false  -profile #{profile} #{file}", inputs.to_hash.merge('add_option_dashes' => true))
-        else
-          cmd("nextflow run -work-dir #{work} -ansi-log false #{file}", inputs.to_hash.merge('add_option_dashes' => true))
-        end
+
+        cmd = "nextflow "
+
+        cmd += " -C #{config_file}" if config_file
+
+        cmd += " run"
+
+        cmd += " -work-dir #{work} -ansi-log false"
+
+        cmd += " -profile #{profile}" if profile
+
+
+        cmd("#{cmd} #{file}", nextflow_inputs.merge('add_option_dashes' => true))
       end
 
       output_file = file(output).glob.first if output

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.33.2
+  version: 5.33.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-02-23 00:00:00.000000000 Z
+date: 2022-02-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake