Fix: Nextflow Samplesheet File Cell Pattern Recognition (#965)

* chore: update samplesheet_component to merge patterns when anyOf is present

* chore: fix file selection for fastq_NUM cells

app/components/nextflow/samplesheet_component.rb

@@ -53,6 +53,16 @@ def sample_samplesheet_params(sample) # rubocop:disable Metrics/CyclomaticComple
       end
     end
 
+    def expected_pattern(entry)
+      if entry.key?('pattern')
+        entry['pattern']
+      elsif entry.key?('anyOf')
+        entry['anyOf'].select do |condition|
+          condition.key?('pattern')
+        end.pluck('pattern').join('|')
+      end
+    end
+
     def file_samplesheet_values(file)
       { form_value: file.empty? ? '' : file[:global_id],
         filename: file.empty? ? I18n.t('nextflow.samplesheet.file_cell_component.no_selected_file') : file[:filename],
@@ -64,11 +74,12 @@ def metadata_samplesheet_values(sample, name)
       { form_value: metadata.empty? ? '' : metadata }
     end
 
-    def extract_properties(schema)
+    def extract_properties(schema) # rubocop:disable Metrics/AbcSize
       @properties = schema['items']['properties']
       @properties.each do |property, entry|
         @properties[property]['required'] = schema['items']['required'].include?(property)
         @properties[property]['cell_type'] = identify_cell_type(property, entry)
+        @properties[property]['pattern'] = expected_pattern(entry)
       end
 
       if @required_properties.include?('fastq_1') && @required_properties.include?('fastq_2')
@@ -83,7 +94,7 @@ def identify_cell_type(property, entry)
 
       return 'sample_name_cell' if property == 'sample_name'
 
-      return 'fastq_cell' if property.match(/fastq_\d+/)
+      return 'fastq_cell' if property.match(/^fastq_\d+$/)
 
       return 'file_cell' if check_for_file(entry)
 

app/models/concerns/file_selector.rb

@@ -41,13 +41,9 @@ def sort_files # rubocop:disable Metrics/MethodLength
   def samplesheet_fastq_files(property, pattern)
     direction = fastq_direction(property)
     singles = filter_files_by_pattern(sorted_files[:singles] || [], pattern || "/^\S+.f(ast)?q(.gz)?$/")
-    files = []
-    if sorted_files[direction].present?
-      files = sorted_files[direction] || []
-      files.concat(singles) if property['pe_only'].blank?
-    else
-      files = singles
-    end
+    files = sorted_files.fetch(direction, [])
+
+    files.concat(singles) if (direction == :pe_forward && property['pe_only'].blank?) || direction == :none
     (files.sort_by! { |file| file[:created_at] }).reverse
   end
 
@@ -58,9 +54,11 @@ def most_recent_fastq_file(property, pattern)
 
     if sorted_files[direction].present?
       sorted_files[direction].last
-    else
+    elsif %i[pe_forward none].include?(direction)
       last_single = filter_files_by_pattern(sorted_files[:singles] || [], pattern || "/^\S+.f(ast)?q(.gz)?$/").last
       last_single.nil? ? {} : last_single
+    else
+      {}
     end
   end
 
@@ -82,6 +80,13 @@ def filter_files_by_pattern(files, pattern)
   private
 
   def fastq_direction(property)
-    property.match(/fastq_(\d+)/)[1].to_i == 1 ? :pe_forward : :pe_reverse
+    case property.match(/^fastq_(\d+)$/).to_a[1]
+    when '1'
+      :pe_forward
+    when '2'
+      :pe_reverse
+    else
+      :single
+    end
   end
 end