feat(illumina-sample-sheet)!: require BCL Convert version and pipeline from the caller

The library no longer decides which BCL Convert version a sample sheet uses.

BREAKING CHANGE: BclConvertSettingsSection requires the software version and
CloudSettingsSection requires the BCL Convert pipeline URN.
BclConvertSoftwareVersion and CloudSettingsSection::BCL_CONVERT_PIPELINE are removed.

🤖 Generated with Claude Code

Author: Lisa Fischer

src/IlluminaSampleSheet/V2/BclConvertSoftwareVersion.php

@@ -3,21 +3,17 @@
 namespace MLL\Utils\IlluminaSampleSheet\V2\Sections;
 
 use Illuminate\Support\Collection;
-use MLL\Utils\IlluminaSampleSheet\V2\BclConvertSoftwareVersion;
 use MLL\Utils\IlluminaSampleSheet\V2\Enums\FastQCompressionFormat;
 
 final class BclConvertSettingsSection extends SimpleKeyValueSection
 {
     use RequiresAnalysisLocationToBeSet;
 
-    private string $cloudSoftwareVersion;
-
-    public function __construct(string $cloudSoftwareVersion = BclConvertSoftwareVersion::V4_1_23)
+    public function __construct(string $softwareVersion)
     {
-        $this->cloudSoftwareVersion = $cloudSoftwareVersion;
-
         $fields = new Collection([
             'FastqCompressionFormat' => FastQCompressionFormat::GZIP,
+            'SoftwareVersion' => $softwareVersion,
         ]);
 
         parent::__construct($fields);
@@ -26,20 +22,9 @@ public function __construct(string $cloudSoftwareVersion = BclConvertSoftwareVer
     public function performAnalysisOn(AnalysisLocation $analysisLocation): void
     {
         $this->analysisLocation = $analysisLocation;
-        $analysisLocation->value === AnalysisLocation::LOCAL_MACHINE
-            ? $this->performAnalysisOnLocalMachine()
-            : $this->performAnalysisOnCloud();
-    }
-
-    private function performAnalysisOnCloud(): void
-    {
-        $this->keyValues['SoftwareVersion'] = $this->cloudSoftwareVersion;
-    }
-
-    private function performAnalysisOnLocalMachine(): void
-    {
-        $this->keyValues['SoftwareVersion'] = BclConvertSoftwareVersion::V4_4_6;
-        $this->keyValues['GenerateFastqcMetrics'] = 'true';
+        if ($analysisLocation->value === AnalysisLocation::LOCAL_MACHINE) {
+            $this->keyValues['GenerateFastqcMetrics'] = 'true';
+        }
     }
 
     public function sectionName(): string

src/IlluminaSampleSheet/V2/Sections/BclConvertSettingsSection.php

@@ -9,10 +9,8 @@ final class CloudSettingsSection extends SimpleKeyValueSection
     /** @var string */
     public const GENERATED_VERSION = '2.6.0.202308300002';
     public const CLOUD_WORKFLOW = 'ica_workflow_1';
-    public const BCL_CONVERT_PIPELINE = 'urn:ilmn:ica:pipeline:d5c7e407-d439-48c8-bce5-b7aec225f6a7#BclConvert_v4_1_23_patch1';
-    public const BCL_CONVERT_PIPELINE_V4_4_10 = 'urn:ilmn:ica:pipeline:4bdae602-abe4-4230-b0c6-f886af563b26#BclConvert_v4_4_10';
 
-    public function __construct(string $bclConvertPipeline = self::BCL_CONVERT_PIPELINE)
+    public function __construct(string $bclConvertPipeline)
     {
         parent::__construct(new Collection([
             'GeneratedVersion' => self::GENERATED_VERSION,

src/IlluminaSampleSheet/V2/Sections/CloudSettingsSection.php

@@ -2,7 +2,6 @@
 
 namespace MLL\Utils\Tests\IlluminaSampleSheet\V2;
 
-use MLL\Utils\IlluminaSampleSheet\V2\BclConvertSoftwareVersion;
 use MLL\Utils\IlluminaSampleSheet\V2\Sections\AnalysisLocation;
 use MLL\Utils\IlluminaSampleSheet\V2\Sections\BclConvertSettingsSection;
 use PHPUnit\Framework\TestCase;
@@ -11,19 +10,7 @@ final class BclConvertSettingsSectionTest extends TestCase
 {
     public function testToStringOnCloud(): void
     {
-        $bclConvertSettingsSection = new BclConvertSettingsSection();
-        $bclConvertSettingsSection->performAnalysisOn(AnalysisLocation::CLOUD());
-        $expected = <<<'CSV'
-FastqCompressionFormat,gzip
-SoftwareVersion,4.1.23
-
-CSV;
-        self::assertSame($expected, $bclConvertSettingsSection->convertSectionToString());
-    }
-
-    public function testToStringOnCloudWithSoftwareVersion(): void
-    {
-        $bclConvertSettingsSection = new BclConvertSettingsSection(BclConvertSoftwareVersion::V4_4_10);
+        $bclConvertSettingsSection = new BclConvertSettingsSection('4.4.10');
         $bclConvertSettingsSection->performAnalysisOn(AnalysisLocation::CLOUD());
         $expected = <<<'CSV'
 FastqCompressionFormat,gzip
@@ -35,7 +22,7 @@ public function testToStringOnCloudWithSoftwareVersion(): void
 
     public function testToStringLocal(): void
     {
-        $bclConvertSettingsSection = new BclConvertSettingsSection();
+        $bclConvertSettingsSection = new BclConvertSettingsSection('4.4.6');
         $bclConvertSettingsSection->performAnalysisOn(AnalysisLocation::LOCAL_MACHINE());
 
         $expected = <<<'CSV'

tests/IlluminaSampleSheet/V2/BclConvertSettingsSectionTest.php

@@ -6,7 +6,6 @@
 use MLL\Utils\Flowcells\NovaSeqX1_5B;
 use MLL\Utils\IlluminaSampleSheet\V2\BclConvert\BclSample;
 use MLL\Utils\IlluminaSampleSheet\V2\BclConvert\OverrideCycles;
-use MLL\Utils\IlluminaSampleSheet\V2\BclConvertSoftwareVersion;
 use MLL\Utils\IlluminaSampleSheet\V2\IlluminaSampleSheetVersion2;
 use MLL\Utils\IlluminaSampleSheet\V2\IndexOrientation;
 use MLL\Utils\IlluminaSampleSheet\V2\InstrumentPlatform;
@@ -92,7 +91,7 @@ public function testNovaSeqXCloudSampleSheetToStringReturnsExpectedResult(): voi
             null
         );
 
-        $bclConvertSettingsSection = new BclConvertSettingsSection(BclConvertSoftwareVersion::V4_4_10);
+        $bclConvertSettingsSection = new BclConvertSettingsSection('4.4.10');
 
         $bclConvertDataSection = new BclConvertDataSection($bclSampleList);
 
@@ -103,7 +102,7 @@ public function testNovaSeqXCloudSampleSheetToStringReturnsExpectedResult(): voi
             $readsSection,
             $bclConvertSettingsSection,
             $bclConvertDataSection,
-            new CloudSettingsSection(CloudSettingsSection::BCL_CONVERT_PIPELINE_V4_4_10),
+            new CloudSettingsSection('urn:ilmn:ica:pipeline:4bdae602-abe4-4230-b0c6-f886af563b26#BclConvert_v4_4_10'),
             new CloudDataSection(new Collection([
                 new CloudDataItem($bclSample0->sampleID, 'test', 'foo'),
                 new CloudDataItem($bclSample1->sampleID, 'test', 'foo'),