Illumina sample sheet v2

CHANGELOG.md

@@ -9,6 +9,12 @@ See [GitHub releases](https://github.com/mll-lab/php-utils/releases).
 
 ## Unreleased
 
+## v1.14.0
+
+### Added
+
+- Support creating Illumina NovaSeq Sample Sheets (V2) for NovaSeqX
+
 ## v1.13.0
 
 ### Added

Makefile

@@ -31,7 +31,7 @@ stan: vendor ## Runs a static analysis with phpstan
 .PHONY: test
 test: vendor ## Runs auto-review, unit, and integration tests with phpunit
 	mkdir --parents .build/phpunit
-	vendor/bin/phpunit --cache-result-file=.build/phpunit/result.cache
+	vendor/bin/phpunit --cache-directory=.build/phpunit
 
 vendor: composer.json
 	composer validate --strict

composer.json

@@ -34,7 +34,7 @@
     "phpstan/phpstan-phpunit": "^1",
     "phpstan/phpstan-strict-rules": "^1",
     "phpunit/phpunit": "^9 || ^10 || ^11",
-    "rector/rector": "^0.17",
+    "rector/rector": "^1",
     "thecodingmachine/phpstan-safe-rule": "^1.2"
   },
   "suggest": {

rector.php

@@ -2,6 +2,7 @@
 
 use Rector\CodeQuality\Rector\Concat\JoinStringConcatRector;
 use Rector\Config\RectorConfig;
+use Rector\PHPUnit\Rector\Class_\PreferPHPUnitSelfCallRector;
 use Rector\Set\ValueObject\SetList;
 
 return static function (RectorConfig $rectorConfig): void {
@@ -17,6 +18,9 @@
             __DIR__ . '/tests/CSVArrayTest.php', // keep `\r\n` for readability
         ],
     ]);
+
+    $rectorConfig->rule(PreferPHPUnitSelfCallRector::class);
+
     $rectorConfig->paths([__DIR__ . '/src', __DIR__ . '/tests']);
     $rectorConfig->phpstanConfig(__DIR__ . '/phpstan.neon');
 };

src/IlluminaSampleSheet/IlluminaSampleSheetException.php

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

src/IlluminaSampleSheet/SampleSheet.php

@@ -0,0 +1,24 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\IlluminaSampleSheet;
+
+abstract class SampleSheet
+{
+    /** @var array<Section> */
+    protected array $sections = [];
+
+    public function addSection(Section $section): void
+    {
+        $this->sections[] = $section;
+    }
+
+    public function toString(): string
+    {
+        $sectionStrings = array_map(
+            fn (Section $section): string => $section->convertSectionToString(),
+            $this->sections
+        );
+
+        return implode("\n", $sectionStrings);
+    }
+}

src/IlluminaSampleSheet/Section.php

@@ -0,0 +1,8 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\IlluminaSampleSheet;
+
+interface Section
+{
+    public function convertSectionToString(): string;
+}

src/IlluminaSampleSheet/V2/BclConvert/BclConvertSection.php

@@ -0,0 +1,28 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\IlluminaSampleSheet\V2\BclConvert;
+
+use MLL\Utils\IlluminaSampleSheet\Section;
+
+class BclConvertSection implements Section
+{
+    protected SettingsSection $settingsSection;
+
+    protected DataSection $dataSection;
+
+    public function __construct(SettingsSection $settingsSection, DataSection $dataSection)
+    {
+        $this->settingsSection = $settingsSection;
+        $this->dataSection = $dataSection;
+    }
+
+    public function convertSectionToString(): string
+    {
+        $bclConvertLines = [
+            $this->settingsSection->convertSectionToString(),
+            $this->dataSection->convertSectionToString(),
+        ];
+
+        return implode("\n", $bclConvertLines);
+    }
+}

src/IlluminaSampleSheet/V2/BclConvert/BclSample.php

@@ -0,0 +1,51 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\IlluminaSampleSheet\V2\BclConvert;
+
+class BclSample
+{
+    public int $lane;
+
+    /** Not using camelCase because the property names of this class must match the CSV file. */
+    public string $sample_ID;
+
+    public string $index;
+
+    public ?string $index2 = null;
+
+    public ?string $overrideCycles = null;
+
+    public ?string $adapterRead1 = null;
+
+    public ?string $adapterRead2 = null;
+
+    public ?string $barcodeMismatchesIndex1 = null;
+
+    public ?string $barcodeMismatchesIndex2 = null;
+
+    public function __construct(
+        int $lane,
+        string $sample_ID,
+        string $index
+    ) {
+        $this->lane = $lane;
+        $this->sample_ID = $sample_ID;
+        $this->index = $index;
+    }
+
+    /** @return array<int|string> */
+    public function toArray(): array
+    {
+        return array_filter([
+            $this->lane,
+            $this->sample_ID,
+            $this->index,
+            $this->index2,
+            $this->overrideCycles,
+            $this->adapterRead1,
+            $this->adapterRead2,
+            $this->barcodeMismatchesIndex1,
+            $this->barcodeMismatchesIndex2,
+        ]);
+    }
+}

src/IlluminaSampleSheet/V2/BclConvert/DataSection.php

@@ -0,0 +1,52 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\IlluminaSampleSheet\V2\BclConvert;
+
+use MLL\Utils\IlluminaSampleSheet\Section;
+
+class DataSection implements Section
+{
+    /** @var array<BclSample> */
+    protected array $dataRows = [];
+
+    public function addSample(BclSample $bclSample): void
+    {
+        $this->dataRows[] = $bclSample;
+    }
+
+    public function convertSectionToString(): string
+    {
+        /** @var array<string> $samplePropertiesOfFirstSample */
+        $samplePropertiesOfFirstSample = array_keys(get_object_vars($this->dataRows[0]));
+        foreach ($this->dataRows as $sample) {
+            $actualProperties = array_keys(get_object_vars($sample));
+            if ($samplePropertiesOfFirstSample !== $actualProperties) {
+                throw new \Exception('All samples must have the same properties. Expected: ' . \Safe\json_encode($samplePropertiesOfFirstSample) . ', Actual: ' . \Safe\json_encode($actualProperties));
+            }
+        }
+
+        $bclConvertDataHeaderLines = $this->generateDataHeaderByProperties($samplePropertiesOfFirstSample);
+
+        $bclConvertDataLines = [
+            '[BCLConvert_Data]',
+            $bclConvertDataHeaderLines,
+        ];
+
+        foreach ($this->dataRows as $dataRow) {
+            $bclConvertDataLines[] = implode(',', $dataRow->toArray());
+        }
+
+        return implode("\n", $bclConvertDataLines) . "\n";
+    }
+
+    /** @param array<string> $samplePropertiesOfFirstSample */
+    protected function generateDataHeaderByProperties(array $samplePropertiesOfFirstSample): string
+    {
+        $samplePropertiesOfFirstSample = array_filter($samplePropertiesOfFirstSample, fn (string $value) // @phpstan-ignore-next-line Variable property access on a non-object required here
+        => $this->dataRows[0]->$value !== null);
+
+        $samplePropertiesOfFirstSample = array_map(fn (string $value) => ucfirst($value), $samplePropertiesOfFirstSample);
+
+        return implode(',', $samplePropertiesOfFirstSample);
+    }
+}

src/IlluminaSampleSheet/V2/BclConvert/SettingsSection.php

@@ -0,0 +1,42 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\IlluminaSampleSheet\V2\BclConvert;
+
+use MLL\Utils\IlluminaSampleSheet\Section;
+use MLL\Utils\IlluminaSampleSheet\V2\Enums\FastQCompressionFormat;
+
+class SettingsSection implements Section
+{
+    public string $softwareVersion;
+
+    public FastQCompressionFormat $fastqCompressionFormat;
+
+    public ?bool $trimUMI = null;
+
+    public function __construct(
+        string $softwareVersion,
+        FastQCompressionFormat $fastqCompressionFormat
+    ) {
+        $this->softwareVersion = $softwareVersion;
+        $this->fastqCompressionFormat = $fastqCompressionFormat;
+    }
+
+    public function convertSectionToString(): string
+    {
+        $bclConvertSettingsLines = [
+            '[BCLConvert_Settings]',
+            "SoftwareVersion,{$this->softwareVersion}",
+            "FastqCompressionFormat,{$this->fastqCompressionFormat->value}",
+        ];
+
+        if (! is_null($this->trimUMI)) {
+            $trimUMIAsString = $this->trimUMI
+                ? '1'
+                : '0';
+
+            $bclConvertSettingsLines[] = "TrimUMI,{$trimUMIAsString}";
+        }
+
+        return implode("\n", $bclConvertSettingsLines) . "\n";
+    }
+}

src/IlluminaSampleSheet/V2/Enums/FastQCompressionFormat.php

@@ -0,0 +1,26 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\IlluminaSampleSheet\V2\Enums;
+
+class FastQCompressionFormat
+{
+    public const GZIP = 'gzip';
+    public const DRAGEN = 'dragen';
+
+    public string $value;
+
+    public function __construct(string $value)
+    {
+        $this->value = $value;
+    }
+
+    public static function GZIP(): self
+    {
+        return new self(self::GZIP);
+    }
+
+    public static function DRAGEN(): self
+    {
+        return new self(self::DRAGEN);
+    }
+}

src/IlluminaSampleSheet/V2/HeaderSection.php

@@ -0,0 +1,56 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\IlluminaSampleSheet\V2;
+
+use MLL\Utils\IlluminaSampleSheet\Section;
+
+class HeaderSection implements Section
+{
+    protected const FILE_FORMAT_VERSION = '2';
+
+    protected string $fileFormatVersion = self::FILE_FORMAT_VERSION;
+
+    public string $runName;
+
+    public ?string $runDescription = null;
+
+    public ?string $instrumentType = null;
+
+    public ?string $instrumentPlatform = null;
+
+    /** @var array<string, string> */
+    protected array $customParams = [];
+
+    public function __construct(string $runName)
+    {
+        $this->runName = $runName;
+    }
+
+    public function setCustomParam(string $paramName, string $paramValue): void
+    {
+        $this->customParams['Custom_' . $paramName] = $paramValue;
+    }
+
+    public function convertSectionToString(): string
+    {
+        $headerLines = [
+            '[Header]',
+            "FileFormatVersion,{$this->fileFormatVersion}",
+            "RunName,{$this->runName}",
+        ];
+        if (! is_null($this->runDescription)) {
+            $headerLines[] = "RunDescription,{$this->runDescription}";
+        }
+        if (! is_null($this->instrumentType)) {
+            $headerLines[] = "InstrumentType,{$this->instrumentType}";
+        }
+        if (! is_null($this->instrumentPlatform)) {
+            $headerLines[] = "InstrumentPlatform,{$this->instrumentPlatform}";
+        }
+        foreach ($this->customParams as $paramName => $paramValue) {
+            $headerLines[] = "{$paramName},{$paramValue}";
+        }
+
+        return implode("\n", $headerLines) . "\n";
+    }
+}

src/IlluminaSampleSheet/V2/NovaSeqXSampleSheet.php

@@ -0,0 +1,21 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\IlluminaSampleSheet\V2;
+
+use MLL\Utils\IlluminaSampleSheet\SampleSheet;
+use MLL\Utils\IlluminaSampleSheet\V2\BclConvert\BclConvertSection;
+
+class NovaSeqXSampleSheet extends SampleSheet
+{
+    public function __construct(
+        HeaderSection $header,
+        ReadsSection $reads,
+        ?BclConvertSection $bclConvertSection
+    ) {
+        $this->addSection($header);
+        $this->addSection($reads);
+        if (! is_null($bclConvertSection)) {
+            $this->addSection($bclConvertSection);
+        }
+    }
+}