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feat(illumina-sample-sheet): require BCL Convert version and pipeline from the caller #96

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Merged
fischerl merged 4 commits into from
Oct 12, 2026
Merged

feat(illumina-sample-sheet): require BCL Convert version and pipeline from the caller #96

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a493ce9
feat(illumina-sample-sheet): use BCL Convert 4.4.10 for NovaSeq X clo…
Oct 6, 2026
1373ed7
ci: ignore advisories blocking PHP 7.4 and 8.0 dev installs
Oct 9, 2026
95d8b77
feat(illumina-sample-sheet): make BCL Convert 4.4.10 opt-in for cloud…
Oct 12, 2026
336f223
feat(illumina-sample-sheet): require BCL Convert version and pipeline…
Oct 12, 2026
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4 changes: 3 additions & 1 deletion composer.json
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,9 @@
"policy": {
"advisories": {
"ignore": [
"laravel/framework"
"laravel/framework",

@fischerl fischerl Oct 12, 2026

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why?

@fischerl fischerl Oct 12, 2026

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Neue Security Advisories blockieren die Dev-Installation unter PHP 7.4 und 8.0: league/flysystem 1.x (über laravel/framework 8) bei 7.4 und 8.0, zbateson/mail-mime-parser < 3.0.6 (über spatie/laravel-ray) bei 7.4. Beide sind nur Dev-Abhängigkeiten.

"league/flysystem",
"zbateson/mail-mime-parser"
]
}
},
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21 changes: 0 additions & 21 deletions src/IlluminaSampleSheet/V2/BclConvertSoftwareVersion.php
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This file was deleted.

21 changes: 5 additions & 16 deletions src/IlluminaSampleSheet/V2/Sections/BclConvertSettingsSection.php
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Original file line number Diff line number Diff line change
Expand Up @@ -3,17 +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;

public function __construct()
public function __construct(string $softwareVersion)
{
$fields = new Collection([
'FastqCompressionFormat' => FastQCompressionFormat::GZIP,
'SoftwareVersion' => $softwareVersion,
]);

parent::__construct($fields);
Expand All @@ -22,20 +22,9 @@ public function __construct()
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'] = BclConvertSoftwareVersion::V4_1_23;
}

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
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5 changes: 2 additions & 3 deletions src/IlluminaSampleSheet/V2/Sections/CloudSettingsSection.php
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Expand Up @@ -9,14 +9,13 @@ 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 function __construct()
public function __construct(string $bclConvertPipeline)
{
parent::__construct(new Collection([
'GeneratedVersion' => self::GENERATED_VERSION,
'Cloud_Workflow' => self::CLOUD_WORKFLOW,
'BCLConvert_Pipeline' => self::BCL_CONVERT_PIPELINE,
'BCLConvert_Pipeline' => $bclConvertPipeline,
]));
}

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6 changes: 3 additions & 3 deletions tests/IlluminaSampleSheet/V2/BclConvertSettingsSectionTest.php
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Expand Up @@ -10,19 +10,19 @@ final class BclConvertSettingsSectionTest extends TestCase
{
public function testToStringOnCloud(): void
{
$bclConvertSettingsSection = new BclConvertSettingsSection();
$bclConvertSettingsSection = new BclConvertSettingsSection('4.4.10');
$bclConvertSettingsSection->performAnalysisOn(AnalysisLocation::CLOUD());
$expected = <<<'CSV'
FastqCompressionFormat,gzip
SoftwareVersion,4.1.23
SoftwareVersion,4.4.10

CSV;
self::assertSame($expected, $bclConvertSettingsSection->convertSectionToString());
}

public function testToStringLocal(): void
{
$bclConvertSettingsSection = new BclConvertSettingsSection();
$bclConvertSettingsSection = new BclConvertSettingsSection('4.4.6');
$bclConvertSettingsSection->performAnalysisOn(AnalysisLocation::LOCAL_MACHINE());

$expected = <<<'CSV'
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8 changes: 4 additions & 4 deletions tests/IlluminaSampleSheet/V2/IlluminaSampleSheetVersion2Test.php
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Expand Up @@ -91,7 +91,7 @@ public function testNovaSeqXCloudSampleSheetToStringReturnsExpectedResult(): voi
null
);

$bclConvertSettingsSection = new BclConvertSettingsSection();
$bclConvertSettingsSection = new BclConvertSettingsSection('4.4.10');

$bclConvertDataSection = new BclConvertDataSection($bclSampleList);

Expand All @@ -102,7 +102,7 @@ public function testNovaSeqXCloudSampleSheetToStringReturnsExpectedResult(): voi
$readsSection,
$bclConvertSettingsSection,
$bclConvertDataSection,
new CloudSettingsSection(),
new CloudSettingsSection('urn:ilmn:ica:pipeline:4bdae602-abe4-4230-b0c6-f886af563b26#BclConvert_v4_4_10'),
new CloudDataSection(new Collection([
new CloudDataItem($bclSample0->sampleID, 'test', 'foo'),
new CloudDataItem($bclSample1->sampleID, 'test', 'foo'),
Expand All @@ -126,7 +126,7 @@ public function testNovaSeqXCloudSampleSheetToStringReturnsExpectedResult(): voi

[BCLConvert_Settings]
FastqCompressionFormat,gzip
SoftwareVersion,4.1.23
SoftwareVersion,4.4.10

[BCLConvert_Data]
Lane,Sample_ID,Index,Index2,OverrideCycles,AdapterRead1,AdapterRead2,BarcodeMismatchesIndex1,BarcodeMismatchesIndex2
Expand All @@ -140,7 +140,7 @@ public function testNovaSeqXCloudSampleSheetToStringReturnsExpectedResult(): voi
[Cloud_Settings]
GeneratedVersion,2.6.0.202308300002
Cloud_Workflow,ica_workflow_1
BCLConvert_Pipeline,urn:ilmn:ica:pipeline:d5c7e407-d439-48c8-bce5-b7aec225f6a7#BclConvert_v4_1_23_patch1
BCLConvert_Pipeline,urn:ilmn:ica:pipeline:4bdae602-abe4-4230-b0c6-f886af563b26#BclConvert_v4_4_10

[Cloud_Data]
Sample_ID,ProjectName,LibraryName
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