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Co-authored-by: Benedikt Franke <[email protected]>
mll-lab · May 3, 2024 · 3852ff6 · 3852ff6
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Showing 8 changed files with 16 additions and 14 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,7 +13,7 @@ See [GitHub releases](https://github.com/mll-lab/php-utils/releases).
 
 ### Added
 
-- Add support for creating Illumina NovaSeq Sample Sheets (V2) for NovaSeqX.
+- Support creating Illumina NovaSeq Sample Sheets (V2) for NovaSeqX
 
 ## v1.13.0
 

diff --git a/src/IlluminaSampleSheet/SampleSheet.php b/src/IlluminaSampleSheet/SampleSheet.php
@@ -14,7 +14,12 @@ public function addSection(SectionInterface $section): void
 
     public function toString(): string
     {
-        return implode("\n", array_map(fn (SectionInterface $section) => $section->convertSectionToString(), $this->sections));
+        $sectionStrings = array_map(
+            fn (SectionInterface $section): string => $section->convertSectionToString(),
+            $this->sections
+        );
+
+        return implode("\n", $sectionStrings);
     }
 
     /** @return array<SectionInterface> */

diff --git a/src/IlluminaSampleSheet/SectionInterface.php b/src/IlluminaSampleSheet/SectionInterface.php
@@ -2,7 +2,7 @@
 
 namespace MLL\Utils\IlluminaSampleSheet;
 
-interface SectionInterface
+interface Section
 {
     public function convertSectionToString(): string;
 }
diff --git a/src/IlluminaSampleSheet/V2/BclConvert/BclSample.php b/src/IlluminaSampleSheet/V2/BclConvert/BclSample.php
@@ -24,7 +24,7 @@ class BclSample
 
     public function __construct(
         int $lane,
-        string $sampleId,
+        string $sampleID,
         string $index
     ) {
         $this->lane = $lane;

diff --git a/src/IlluminaSampleSheet/V2/BclConvert/DataSection.php b/src/IlluminaSampleSheet/V2/BclConvert/DataSection.php
@@ -9,9 +9,8 @@ class DataSection implements SectionInterface
     /** @var array<BclSample> */
     private array $dataRows = [];
 
-    public function addSample(
-        BclSample $bclSample
-    ): void {
+    public function addSample(BclSample $bclSample): void
+    {
         $this->dataRows[] = $bclSample;
     }
 

diff --git a/src/IlluminaSampleSheet/V2/HeaderSection.php b/src/IlluminaSampleSheet/V2/HeaderSection.php
@@ -56,7 +56,7 @@ public function convertSectionToString(): string
     {
         $headerLines = [
             '[Header]',
-            'FileFormatVersion,' . $this->fileFormatVersion,
+            "FileFormatVersion,{$this->fileFormatVersion}",
             "RunName,{$this->runName}",
         ];
         if (! is_null($this->runDescription)) {

diff --git a/tests/IlluminaSampleSheet/SampleSheetTest.php b/tests/IlluminaSampleSheet/SampleSheetTest.php
@@ -6,7 +6,7 @@
 use MLL\Utils\IlluminaSampleSheet\SectionInterface;
 use PHPUnit\Framework\TestCase;
 
-class SampleSheetTest extends TestCase
+final class SampleSheetTest extends TestCase
 {
     public function testSampleSheetToStringReturnsCorrectFormat(): void
     {

diff --git a/tests/IlluminaSampleSheet/V2/NovaSeqXCloudSampleSheetTest.php b/tests/IlluminaSampleSheet/V2/NovaSeqXCloudSampleSheetTest.php
@@ -12,13 +12,11 @@
 use MLL\Utils\IlluminaSampleSheet\V2\ReadsSection;
 use PHPUnit\Framework\TestCase;
 
-class NovaSeqXCloudSampleSheetTest extends TestCase
+final class NovaSeqXCloudSampleSheetTest extends TestCase
 {
     public function testNovaSeqXCloudSampleSheetToStringReturnsExpectedResult(): void
     {
-        $headerSection = new HeaderSection(
-            'Run1',
-        );
+        $headerSection = new HeaderSection('Run1');
         $headerSection->setInstrumentPlatform('NovaSeqXSeries');
         $headerSection->setCustomParam('IndexOrientation', 'Orientation1');
 
@@ -88,6 +86,6 @@ public function testNovaSeqXCloudSampleSheetToStringReturnsExpectedResult(): voi
 3,Sample3,Index5,Index6,Cycles3,Adapter5,Adapter6
 ';
 
-        self::assertEquals($expected, $novaSeqXCloudSampleSheet->toString());
+        self::assertSame($expected, $novaSeqXCloudSampleSheet->toString());
     }
 }