feat(samplesheet)!: Update Illumina sample sheets for NovaSeq X and cloud support

src/Flowcells/FlowcellLaneDoesNotExistException.php

@@ -0,0 +1,5 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+class FlowcellLaneDoesNotExistException extends \Exception {}

src/Flowcells/FlowcellType.php

@@ -0,0 +1,39 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+abstract class FlowcellType
+{
+    abstract public function name(): string;
+
+    abstract public function totalLaneCount(): int;
+
+    /** @var array<int, int> */
+    public array $lanes;
+
+    /** @param array<int, int>|null $lanes */
+    public function __construct(?array $lanes)
+    {
+        if ($lanes === null) {
+            $lanes = range(1, $this->totalLaneCount());
+        }
+        $this->validate($lanes);
+        $this->lanes = $lanes;
+    }
+
+    /** @param array<int, int> $specificLanes */
+    public function validate(array $specificLanes): void
+    {
+        $validLanes = range(1, $this->totalLaneCount());
+        $invalidLanes = array_diff($specificLanes, $validLanes);
+
+        if (count($invalidLanes) > 0) {
+            $label = count($invalidLanes) > 1
+                ? 'lanes'
+                : 'lane';
+            $invalidLanesAsString = implode(', ', $invalidLanes);
+
+            throw new FlowcellLaneDoesNotExistException("The Flowcell-Type: '{$this->name()}' doesn't contain {$label}: {$invalidLanesAsString}");
+        }
+    }
+}

src/Flowcells/Miseqi100_100M.php

@@ -0,0 +1,16 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+class Miseqi100_100M extends FlowcellType
+{
+    public function totalLaneCount(): int
+    {
+        return 1;
+    }
+
+    public function name(): string
+    {
+        return '100M';
+    }
+}

src/Flowcells/Miseqi100_25M.php

@@ -0,0 +1,16 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+class Miseqi100_25M extends FlowcellType
+{
+    public function totalLaneCount(): int
+    {
+        return 1;
+    }
+
+    public function name(): string
+    {
+        return '25M';
+    }
+}

src/Flowcells/Miseqi100_50M.php

@@ -0,0 +1,16 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+class Miseqi100_50M extends FlowcellType
+{
+    public function totalLaneCount(): int
+    {
+        return 1;
+    }
+
+    public function name(): string
+    {
+        return '50M';
+    }
+}

src/Flowcells/Miseqi100_5M.php

@@ -0,0 +1,16 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+class Miseqi100_5M extends FlowcellType
+{
+    public function totalLaneCount(): int
+    {
+        return 1;
+    }
+
+    public function name(): string
+    {
+        return '5M';
+    }
+}

src/Flowcells/NovaSeqX10B.php

@@ -0,0 +1,16 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+class NovaSeqX10B extends FlowcellType
+{
+    public function totalLaneCount(): int
+    {
+        return 8;
+    }
+
+    public function name(): string
+    {
+        return '10B';
+    }
+}

src/Flowcells/NovaSeqX1_5B.php

@@ -0,0 +1,16 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+class NovaSeqX1_5B extends FlowcellType
+{
+    public function totalLaneCount(): int
+    {
+        return 2;
+    }
+
+    public function name(): string
+    {
+        return '1.5B';
+    }
+}

src/Flowcells/NovaSeqX25B.php

@@ -0,0 +1,16 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+class NovaSeqX25B extends FlowcellType
+{
+    public function totalLaneCount(): int
+    {
+        return 8;
+    }
+
+    public function name(): string
+    {
+        return '25B';
+    }
+}

src/Flowcells/NovaSeqX5B.php

@@ -0,0 +1,16 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Flowcells;
+
+class NovaSeqX5B extends FlowcellType
+{
+    public function totalLaneCount(): int
+    {
+        return 8;
+    }
+
+    public function name(): string
+    {
+        return '5B';
+    }
+}

src/IlluminaSampleSheet/BaseSampleSheet.php

@@ -15,7 +15,7 @@ public function addSection(Section $section): void
     public function toString(): string
     {
         $sectionStrings = array_map(
-            fn (Section $section): string => $section->convertSectionToString(),
+            fn (Section $section): string => "[{$section->sectionName()}]" . PHP_EOL . $section->convertSectionToString(),
             $this->sections
         );
 

src/IlluminaSampleSheet/Section.php

@@ -5,4 +5,6 @@
 interface Section
 {
     public function convertSectionToString(): string;
+
+    public function sectionName(): string;
 }

src/IlluminaSampleSheet/V1/DataSection.php

@@ -48,7 +48,7 @@ public function convertSectionToString(): string
             ->map(fn (Row $row): string => $row->toString())
             ->implode("\n");
 
-        return "[Data]\n{$firstRow->headerLine()}\n{$rowsData}\n";
+        return "{$firstRow->headerLine()}\n{$rowsData}\n";
     }
 
     protected function validateDuplicatedSampleIDs(): void
@@ -65,4 +65,9 @@ protected function validateDuplicatedSampleIDs(): void
             throw new IlluminaSampleSheetException("Sample_ID values must be distinct. Duplicated SampleIDs: {$duplicateIDsAsString}");
         }
     }
+
+    public function sectionName(): string
+    {
+        return 'Data';
+    }
 }

src/IlluminaSampleSheet/V1/HeaderSection.php

@@ -49,7 +49,6 @@ public function __construct(
     public function convertSectionToString(): string
     {
         $headerLines = [
-            '[Header]',
             "IEMFileVersion,{$this->iemFileVersion}",
             "Investigator Name,{$this->investigatorName}",
             "Experiment Name,{$this->experimentName}",
@@ -63,4 +62,9 @@ public function convertSectionToString(): string
 
         return implode("\n", $headerLines);
     }
+
+    public function sectionName(): string
+    {
+        return 'Header';
+    }
 }

src/IlluminaSampleSheet/V1/ReadsSection.php

@@ -18,6 +18,11 @@ public function __construct(int $read1Cycles, int $read2Cycles)
 
     public function convertSectionToString(): string
     {
-        return "[Reads]\n" . $this->read1Cycles . "\n" . $this->read2Cycles;
+        return $this->read1Cycles . "\n" . $this->read2Cycles;
+    }
+
+    public function sectionName(): string
+    {
+        return 'Reads';
     }
 }

src/IlluminaSampleSheet/V1/SettingsSection.php

@@ -18,7 +18,7 @@ public function __construct(?string $adapter = null, ?string $adapterRead2 = nul
 
     public function convertSectionToString(): string
     {
-        $settingsLines = ['[Settings]'];
+        $settingsLines = [];
 
         if ($this->adapter !== null) {
             $settingsLines[] = 'Adapter,' . $this->adapter;
@@ -30,4 +30,9 @@ public function convertSectionToString(): string
 
         return implode("\n", $settingsLines);
     }
+
+    public function sectionName(): string
+    {
+        return 'Settings';
+    }
 }