From a6aa6c5d4d9de080a0c5ee55ebbf278bda92f597 Mon Sep 17 00:00:00 2001
From: Josh Adam <josh.adam@phac-aspc.gc.ca>
Date: Wed, 11 Sep 2024 10:20:08 -0500
Subject: [PATCH] ColumnComponent: Exclude non-fastq files if no fastq are
 present (#742)

* fix: Include non-fastq files if none are present

* chore: Fixed typo resulting in error

* chore: Don't render single files if no fastq are available

* chore: Ensure singles are only add if it is not pe only

* chore: Updated to use filter_files_by_pattern

* chore: Fixed parameters
---
 .../nextflow/samplesheet/column_component.rb  | 46 +++++++++++++------
 .../nextflow/samplesheet_component.rb         |  4 ++
 2 files changed, 37 insertions(+), 13 deletions(-)

diff --git a/app/components/nextflow/samplesheet/column_component.rb b/app/components/nextflow/samplesheet/column_component.rb
index 9f1686a3a1..214fedbaba 100644
--- a/app/components/nextflow/samplesheet/column_component.rb
+++ b/app/components/nextflow/samplesheet/column_component.rb
@@ -38,21 +38,41 @@ def render_cell_type(property, entry, sample, fields, index) # rubocop:disable M
       end
 
       def render_fastq_cell(sample, property, entry, fields, index)
-        direction = property.match(/fastq_(\d+)/)[1].to_i == 1 ? :pe_forward : :pe_reverse
-        files = sample.sorted_files[direction] || []
-        data = {}
-        if files.empty? && property != 'fastq_2'
-          files = sample.sorted_files[:singles] || []
+        direction = get_fastq_direction(property)
+        files = get_fastq_files(entry, sample, direction, pe_only: property['pe_only'].present?)
+        data = get_fastq_data(files, direction, index, property)
+        render_file_cell(property, entry, fields, files, @required, data, files&.first)
+      end
+
+      private
+
+      def get_fastq_direction(property)
+        property.match(/fastq_(\d+)/)[1].to_i == 1 ? :pe_forward : :pe_reverse
+      end
+
+      def get_fastq_files(entry, sample, direction, pe_only: false)
+        singles = filter_files_by_pattern(sample.sorted_files[:singles] || [],
+                                          entry['pattern'] || "/^\S+.f(ast)?q(.gz)?$/")
+
+        files = []
+        if sample.sorted_files[direction].present?
+          files = sample.sorted_files[direction] || []
+          files.concat(singles) unless pe_only
         else
-          data = {
-            'data-action' => 'change->nextflow--samplesheet#file_selected',
-            'data-nextflow--samplesheet-target' => "select#{direction.to_s.sub!('pe_', '').capitalize}",
-            'data-direction' => direction.to_s,
-            'data-index' => index
-          }
+          files = singles
         end
-        render_file_cell(property, entry, fields, files,
-                         @required, data, files.nil? ? nil : files.first)
+        files
+      end
+
+      def get_fastq_data(files, direction, index, property)
+        return {} if files.empty? && property == 'fastq_2'
+
+        {
+          'data-action' => 'change->nextflow--samplesheet#file_selected',
+          'data-nextflow--samplesheet-target' => "select#{direction.to_s.sub!('pe_', '').capitalize}",
+          'data-direction' => direction.to_s,
+          'data-index' => index
+        }
       end
 
       def render_other_file_cell(sample, property, entry, fields)
diff --git a/app/components/nextflow/samplesheet_component.rb b/app/components/nextflow/samplesheet_component.rb
index 03c2d3c361..04dc2c9fce 100644
--- a/app/components/nextflow/samplesheet_component.rb
+++ b/app/components/nextflow/samplesheet_component.rb
@@ -24,6 +24,10 @@ def extract_properties(schema)
         @properties[property]['cell_type'] = identify_cell_type(property, entry)
       end
 
+      if @required_properties.include?('fastq_1') && @required_properties.include?('fastq_2')
+        @properties['fastq_1']['pe_only'] = true
+      end
+
       identify_autopopulated_file_properties
     end