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Add test samplesheets for samplesheetparser modules #2013

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2 changes: 2 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -496,6 +496,8 @@ The earth sciences folder contain subfolders for different data formats encounte
- bcl:
- flowcell.tar.gz: bcl data generated on a MiSeq sequencer. Contains only data for the first tile.
- flowcell_samplesheet.csv: SampleSheet for data on flowcell
- flowcell_samplesheet.v1.csv: Illumina SampleSheet in IEM V1 (bcl2fastq) format — dual-index, 5 samples across 2 projects and 2 lanes
- flowcell_samplesheet.v2.csv: Illumina SampleSheet in BCLConvert V2 format — dual-index, 5 samples across 2 projects and 2 lanes
- cram:
- test.paired*end.sorted: Mapped, and sorted reads based on `test*{1,2}` (normal)
- test.paired*end.markduplicates.sorted: Mapped, sorted, and duplicate marked reads based on `test*{1,2}` (normal)
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27 changes: 27 additions & 0 deletions data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.v1.csv
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[Header]
IEMFileVersion,5
Experiment Name,240115_A01234_0042_AHJLG7DRXX
Date,2024-01-15
Workflow,GenerateFASTQ
Application,FASTQ Only
Instrument Type,NovaSeq 6000
Assay,TruSeq DNA PCR-Free
Index Adapters,TruSeq DNA UD Indexes (96 Indexes)
Chemistry,Amplicon

[Reads]
151
151

[Settings]
ReverseComplement,0
Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
1,Sample1,SampleOne,,A01,UDP0001,CAAGACAGAT,UDP0001,ACTATAGCCT,ProjectAlpha,WGS_batch1
1,Sample2,SampleTwo,,B01,UDP0002,TGAACCTGAT,UDP0002,TGATACGTCC,ProjectAlpha,WGS_batch1
1,Sample3,SampleThree,,C01,UDP0003,GCACAACGTT,UDP0003,CATCTCACAG,ProjectAlpha,WGS_batch1
2,Sample4,SampleFour,,D01,UDP0004,ATCGCCTGTT,UDP0004,GACTAGCATG,ProjectBeta,WGS_batch2
2,Sample5,SampleFive,,E01,UDP0005,CTTGTAGCAA,UDP0005,TGCGTCAGCC,ProjectBeta,WGS_batch2
24 changes: 24 additions & 0 deletions data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.v2.csv
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[Header]
FileFormatVersion,2
RunName,240115_LH00336_0025_A227HGJLT3
InstrumentPlatform,NovaSeqXSeries

[Reads]
Read1Cycles,151
Read2Cycles,151
Index1Cycles,10
Index2Cycles,10

[BCLConvert_Settings]
SoftwareVersion,3.9.3
AdapterRead1,CTGTCTCTTATACACATCT
AdapterRead2,CTGTCTCTTATACACATCT
OverrideCycles,Y151;I10;I10;Y151

[BCLConvert_Data]
Lane,Sample_ID,Sample_Name,Index,Index2,Sample_Project
1,Sample1,SampleOne,ATTACTCGAT,TATAGCCTGT,ProjectAlpha
1,Sample2,SampleTwo,TCCGGAGACC,ATAGAGGCAC,ProjectAlpha
1,Sample3,SampleThree,TAGGCATGCA,CCTATCCTAG,ProjectAlpha
2,Sample4,SampleFour,CTCTCTACGC,GGCTCTGAGA,ProjectBeta
2,Sample5,SampleFive,CGGAGCCTAA,AGGCGAAGAG,ProjectBeta