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AmandaBirminghamAmandaBirmingham
committed
add test for sif generation from sample sheet with samplecontext
1 parent f7cc35b commit f941664

5 files changed

+325
-13
lines changed

‎tests/data/good_sheet_w_replicates_and_context.csv

Lines changed: 103 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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1+
[Header],,,,,,,,,,,,
2+
IEMFileVersion,4,,,,,,,,,,,
3+
SheetType,standard_metag,,,,,,,,,,,
4+
SheetVersion,101,,,,,,,,,,,
5+
Investigator Name,Knight,,,,,,,,,,,
6+
Experiment Name,RKL0042,,,,,,,,,,,
7+
Date,2/26/20,,,,,,,,,,,
8+
Workflow,GenerateFASTQ,,,,,,,,,,,
9+
Application,FASTQ Only,,,,,,,,,,,
10+
Assay,Metagenomic,,,,,,,,,,,
11+
Description,,,,,,,,,,,,
12+
Chemistry,Default,,,,,,,,,,,
13+
,,,,,,,,,,,,
14+
[Reads],,,,,,,,,,,,
15+
150,,,,,,,,,,,,
16+
150,,,,,,,,,,,,
17+
,,,,,,,,,,,,
18+
[Settings],,,,,,,,,,,,
19+
ReverseComplement,0,,,,,,,,,,,
20+
,,,,,,,,,,,,
21+
[Data],,,,,,,,,,,,
22+
orig_name,Sample_ID,Sample_Name,source_well_384,destination_well_384,Sample_Plate,well_id_384,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Well_description
23+
BLANK.43.12G,BLANK_43_12G_A1,BLANK.43.12G.A1,A1,A1,Feist_11661_P43,A1,iTru7_114_08,CCGACTAT,iTru5_01_A,AAGGCTGA,Feist_11661,blue_quadrant
24+
BLANK.43.12H,BLANK_43_12H_A3,BLANK.43.12H.A3,A3,A3,Feist_11661_P43,A3,iTru7_114_09,ACCGACAA,iTru5_02_A,CGATCGAT,Feist_11661,blue_quadrant
25+
TMI.test.1,TMI_test_1_A5,TMI.test.1.A5,A5,A5,Feist_11661_P43,A5,iTru7_114_10,CCGACTAT,iTru5_03_A,TTACCGAG,TMI_10317,blue_quadrant
26+
Other.test.2,Other_test_2_A7,Other.test.2.A7,A7,A7,Feist_11661_P43,A7,iTru7_114_11,CTTCGCAA,iTru5_04_A,AAGACACC,Other_11223,blue_quadrant
27+
RMA.KHP.rpoS.Mage.Q97N,RMA_KHP_rpoS_Mage_Q97N_A9,RMA.KHP.rpoS.Mage.Q97N.A9,A9,A9,Feist_11661_P43,A9,iTru7_114_12,GCCTTGTT,iTru5_05_A,GTCCTAAG,Feist_11661,blue_quadrant
28+
RMA.KHP.rpoS.Mage.Q97E,RMA_KHP_rpoS_Mage_Q97E_A11,RMA.KHP.rpoS.Mage.Q97E.A11,A11,A11,Feist_11661_P43,A11,iTru7_201_01,AACACCAC,iTru5_06_A,CATCTGCT,Feist_11661,blue_quadrant
29+
JBI.KHP.HGL.021,JBI_KHP_HGL_021_A13,JBI.KHP.HGL.021.A13,A13,A13,Feist_11661_P43,A13,iTru7_201_02,AACTTGCC,iTru5_07_A,GAAGGTTC,Feist_11661,blue_quadrant
30+
JBI.KHP.HGL.022,JBI_KHP_HGL_022_A15,JBI.KHP.HGL.022.A15,A15,A15,Feist_11661_P43,A15,iTru7_201_03,CGTATCTC,iTru5_08_A,CTCTCAGA,Feist_11661,blue_quadrant
31+
JBI.KHP.HGL.023,JBI_KHP_HGL_023_A17,JBI.KHP.HGL.023.A17,A17,A17,Feist_11661_P43,A17,iTru7_201_04,CAATGTGG,iTru5_09_A,GAAGAGGT,Feist_11661,blue_quadrant
32+
JBI.KHP.HGL.024,JBI_KHP_HGL_024_A19,JBI.KHP.HGL.024.A19,A19,A19,Feist_11661_P43,A19,iTru7_201_05,GGTACGAA,iTru5_10_A,TCGTCTGA,Feist_11661,blue_quadrant
33+
AP581451B02,AP581451B02_A21,AP581451B02.A21,A21,A21,NYU_BMS_Melanoma_13059_P1,A21,iTru7_108_05,TCTGAGAG,iTru5_09_A,CTCTCAGA,NYU_BMS_Melanoma_13059,blue_quadrant
34+
EP256645B01,EP256645B01_A23,EP256645B01.A23,A23,A23,NYU_BMS_Melanoma_13059_P1,A23,iTru7_108_06,ACCGCATA,iTru5_10_A,TCGTCTGA,NYU_BMS_Melanoma_13059,blue_quadrant
35+
EP112567B02,EP112567B02_C1,EP112567B02.C1,C1,C1,NYU_BMS_Melanoma_13059_P1,C1,iTru7_108_07,GAAGTACC,iTru5_11_A,CAATAGCC,NYU_BMS_Melanoma_13059,blue_quadrant
36+
EP337425B01,EP337425B01_C3,EP337425B01.C3,C3,C3,NYU_BMS_Melanoma_13059_P1,C3,iTru7_108_08,CAGGTATC,iTru5_12_A,CATTCGTC,NYU_BMS_Melanoma_13059,blue_quadrant
37+
LP127890A01,LP127890A01_C5,LP127890A01.C5,C5,C5,NYU_BMS_Melanoma_13059_P1,C5,iTru7_108_09,TCTCTAGG,iTru5_01_B,AGTGGCAA,NYU_BMS_Melanoma_13059,blue_quadrant
38+
EP159692B04,EP159692B04_C7,EP159692B04.C7,C7,C7,NYU_BMS_Melanoma_13059_P1,C7,iTru7_108_10,AAGCACTG,iTru5_02_B,GTGGTATG,NYU_BMS_Melanoma_13059,blue_quadrant
39+
EP987683A01,EP987683A01_C9,EP987683A01.C9,C9,C9,NYU_BMS_Melanoma_13059_P1,C9,iTru7_108_11,CCAAGCAA,iTru5_03_B,TGAGCTGT,NYU_BMS_Melanoma_13059,blue_quadrant
40+
AP959450A03,AP959450A03_C11,AP959450A03.C11,C11,C11,NYU_BMS_Melanoma_13059_P1,C11,iTru7_108_12,TGTTCGAG,iTru5_04_B,CGTCAAGA,NYU_BMS_Melanoma_13059,blue_quadrant
41+
SP464350A04,SP464350A04_C13,SP464350A04.C13,C13,C13,NYU_BMS_Melanoma_13059_P1,C13,iTru7_109_01,CTCGTCTT,iTru5_05_B,AAGCATCG,NYU_BMS_Melanoma_13059,blue_quadrant
42+
EP121011B01,EP121011B01_C15,EP121011B01.C15,C15,C15,NYU_BMS_Melanoma_13059_P1,C15,iTru7_109_04,TCGGTTAC,iTru5_08_B,ACCTCTTC,NYU_BMS_Melanoma_13059,blue_quadrant
43+
BLANK.43.12G,BLANK_43_12G_A2,BLANK.43.12G.A2,A1,A2,Feist_11661_P43,A2,iTru7_114_08,TCTGAGAG,iTru5_01_A,AAGCACTG,Feist_11661,green_quadrant
44+
BLANK.43.12H,BLANK_43_12H_A4,BLANK.43.12H.A4,A3,A4,Feist_11661_P43,A4,iTru7_114_09,CAATAGCC,iTru5_02_A,CGTCAAGA,Feist_11661,green_quadrant
45+
TMI.test.1,TMI_test_1_A6,TMI.test.1.A6,A5,A6,Feist_11661_P43,A6,iTru7_114_10,ACCGCATA,iTru5_03_A,CCAAGCAA,TMI_10317,green_quadrant
46+
Other.test.2,Other_test_2_A8,Other.test.2.A8,A7,A8,Feist_11661_P43,A8,iTru7_114_11,CATTCGTC,iTru5_04_A,AAGCATCG,Other_11223,green_quadrant
47+
RMA.KHP.rpoS.Mage.Q97N,RMA_KHP_rpoS_Mage_Q97N_A10,RMA.KHP.rpoS.Mage.Q97N.A10,A9,A10,Feist_11661_P43,A10,iTru7_114_12,GAAGTACC,iTru5_05_A,TGTTCGAG,Feist_11661,green_quadrant
48+
RMA.KHP.rpoS.Mage.Q97E,RMA_KHP_rpoS_Mage_Q97E_A12,RMA.KHP.rpoS.Mage.Q97E.A12,A11,A12,Feist_11661_P43,A12,iTru7_201_01,AGTGGCAA,iTru5_06_A,TACTCCAG,Feist_11661,green_quadrant
49+
JBI.KHP.HGL.021,JBI_KHP_HGL_021_A14,JBI.KHP.HGL.021.A14,A13,A14,Feist_11661_P43,A14,iTru7_201_02,CAGGAATC,iTru5_07_A,CTCGTCTT,Feist_11661,green_quadrant
50+
JBI.KHP.HGL.022,JBI_KHP_HGL_022_A16,JBI.KHP.HGL.022.A16,A15,A16,Feist_11661_P43,A16,iTru7_201_03,GTGGAATG,iTru5_08_A,GATACCTG,Feist_11661,green_quadrant
51+
JBI.KHP.HGL.023,JBI_KHP_HGL_023_A18,JBI.KHP.HGL.023.A18,A17,A18,Feist_11661_P43,A18,iTru7_201_04,TCTCAAGG,iTru5_09_A,CGAACTGT,Feist_11661,green_quadrant
52+
JBI.KHP.HGL.024,JBI_KHP_HGL_024_A20,JBI.KHP.HGL.024.A20,A19,A20,Feist_11661_P43,A20,iTru7_201_05,TGAGATGT,iTru5_10_A,ACCTCTTC,Feist_11661,green_quadrant
53+
AP581451B02,AP581451B02_A22,AP581451B02.A22,A21,A22,NYU_BMS_Melanoma_13059_P1,A22,iTru7_108_05,TCTGAAAG,iTru5_09_A,ATCTCAGA,NYU_BMS_Melanoma_13059,green_quadrant
54+
EP256645B01,EP256645B01_A24,EP256645B01.A24,A23,A24,NYU_BMS_Melanoma_13059_P1,A24,iTru7_108_06,ACAGCATA,iTru5_10_A,TGGTCTGA,NYU_BMS_Melanoma_13059,green_quadrant
55+
EP112567B02,EP112567B02_C2,EP112567B02.C2,C1,C2,NYU_BMS_Melanoma_13059_P1,C2,iTru7_108_07,GAAATACC,iTru5_11_A,CATTAGCC,NYU_BMS_Melanoma_13059,green_quadrant
56+
EP337425B01,EP337425B01_C4,EP337425B01.C4,C3,C4,NYU_BMS_Melanoma_13059_P1,C4,iTru7_108_08,CAGATATC,iTru5_12_A,CAGTCGTC,NYU_BMS_Melanoma_13059,green_quadrant
57+
LP127890A01,LP127890A01_C6,LP127890A01.C6,C5,C6,NYU_BMS_Melanoma_13059_P1,C6,iTru7_108_09,TCTATAGG,iTru5_01_B,AGTCGCAA,NYU_BMS_Melanoma_13059,green_quadrant
58+
EP159692B04,EP159692B04_C8,EP159692B04.C8,C7,C8,NYU_BMS_Melanoma_13059_P1,C8,iTru7_108_10,AAGTTATG,iTru5_02_B,GTGGAATG,NYU_BMS_Melanoma_13059,green_quadrant
59+
EP987683A01,EP987683A01_C10,EP987683A01.C10,C9,C10,NYU_BMS_Melanoma_13059_P1,C10,iTru7_108_11,ACAAGCAA,iTru5_03_B,TGAGCTGT,NYU_BMS_Melanoma_13059,green_quadrant
60+
AP959450A03,AP959450A03_C12,AP959450A03.C12,C11,C12,NYU_BMS_Melanoma_13059_P1,C12,iTru7_108_12,AGTTCGAG,iTru5_04_B,CGTCCAGA,NYU_BMS_Melanoma_13059,green_quadrant
61+
SP464350A04,SP464350A04_C14,SP464350A04.C14,C13,C14,NYU_BMS_Melanoma_13059_P1,C14,iTru7_109_01,ATCGTCTT,iTru5_05_B,AAGAATCG,NYU_BMS_Melanoma_13059,green_quadrant
62+
EP121011B01,EP121011B01_C16,EP121011B01.C16,C15,C16,NYU_BMS_Melanoma_13059_P1,C16,iTru7_109_04,ACGGTTAC,iTru5_08_B,ACCACTTC,NYU_BMS_Melanoma_13059,green_quadrant
63+
BLANK.43.12G,BLANK_43_12G_B2,BLANK.43.12G.B2,A1,B2,Feist_11661_P43,B2,iTru7_114_08,AATTCGGT,iTru5_01_A,GTATTAGC,Feist_11661,yellow_quadrant
64+
BLANK.43.12H,BLANK_43_12H_B4,BLANK.43.12H.B4,A3,B4,Feist_11661_P43,B4,iTru7_114_09,TCGGACTT,iTru5_02_A,CACTGAAG,Feist_11661,yellow_quadrant
65+
TMI.test.1,TMI_test_1_B6,TMI.test.1.B6,A5,B6,Feist_11661_P43,B6,iTru7_114_10,TCGGTAAC,iTru5_03_A,AGTCGCTT,TMI_10317,yellow_quadrant
66+
Other.test.2,Other_test_2_B8,Other.test.2.B8,A7,B8,Feist_11661_P43,B8,iTru7_114_11,CATGTGTG,iTru5_04_A,CACAGGAA,Other_11223,yellow_quadrant
67+
RMA.KHP.rpoS.Mage.Q97N,RMA_KHP_rpoS_Mage_Q97N_B10,RMA.KHP.rpoS.Mage.Q97N.B10,A9,B10,Feist_11661_P43,B10,iTru7_114_12,AAGTCGAG,iTru5_05_A,TGGCACTA,Feist_11661,yellow_quadrant
68+
RMA.KHP.rpoS.Mage.Q97E,RMA_KHP_rpoS_Mage_Q97E_B12,RMA.KHP.rpoS.Mage.Q97E.B12,A11,B12,Feist_11661_P43,B12,iTru7_201_01,TGCCTCAA,iTru5_06_A,CCATGAAC,Feist_11661,yellow_quadrant
69+
JBI.KHP.HGL.021,JBI_KHP_HGL_021_B14,JBI.KHP.HGL.021.B14,A13,B14,Feist_11661_P43,B14,iTru7_201_02,TATCGGTC,iTru5_07_A,GGTTGTCA,Feist_11661,yellow_quadrant
70+
JBI.KHP.HGL.022,JBI_KHP_HGL_022_B16,JBI.KHP.HGL.022.B16,A15,B16,Feist_11661_P43,B16,iTru7_201_03,ATCTGACC,iTru5_08_A,GCCAATAC,Feist_11661,yellow_quadrant
71+
JBI.KHP.HGL.023,JBI_KHP_HGL_023_B18,JBI.KHP.HGL.023.B18,A17,B18,Feist_11661_P43,B18,iTru7_201_04,TATTCGCC,iTru5_09_A,AACCTCCT,Feist_11661,yellow_quadrant
72+
JBI.KHP.HGL.024,JBI_KHP_HGL_024_B20,JBI.KHP.HGL.024.B20,A19,B20,Feist_11661_P43,B20,iTru7_201_05,CACAGACT,iTru5_10_A,AGCTACCA,Feist_11661,yellow_quadrant
73+
AP581451B02,AP581451B02_B22,AP581451B02.B22,A21,B22,NYU_BMS_Melanoma_13059_P1,B22,iTru7_108_05,GCTGAGAG,iTru5_09_A,CTCTCAGA,NYU_BMS_Melanoma_13059,yellow_quadrant
74+
EP256645B01,EP256645B01_B24,EP256645B01.B24,A23,B24,NYU_BMS_Melanoma_13059_P1,B24,iTru7_108_06,GCCGCATA,iTru5_10_A,TCGTCTGA,NYU_BMS_Melanoma_13059,yellow_quadrant
75+
EP112567B02,EP112567B02_D2,EP112567B02.D2,C1,D2,NYU_BMS_Melanoma_13059_P1,D2,iTru7_108_07,GGAGTACC,iTru5_11_A,CAATAGCC,NYU_BMS_Melanoma_13059,yellow_quadrant
76+
EP337425B01,EP337425B01_D4,EP337425B01.D4,C3,D4,NYU_BMS_Melanoma_13059_P1,D4,iTru7_108_08,CGGGTATC,iTru5_12_A,CATTCGTC,NYU_BMS_Melanoma_13059,yellow_quadrant
77+
LP127890A01,LP127890A01_D6,LP127890A01.D6,C5,D6,NYU_BMS_Melanoma_13059_P1,D6,iTru7_108_09,TGTCTAGG,iTru5_01_B,AGTGGCAA,NYU_BMS_Melanoma_13059,yellow_quadrant
78+
EP159692B04,EP159692B04_D8,EP159692B04.D8,C7,D8,NYU_BMS_Melanoma_13059_P1,D8,iTru7_108_10,AGGCACTG,iTru5_02_B,GTGGTATG,NYU_BMS_Melanoma_13059,yellow_quadrant
79+
EP987683A01,EP987683A01_D10,EP987683A01.D10,C9,D10,NYU_BMS_Melanoma_13059_P1,D10,iTru7_108_11,GCAAGCAA,iTru5_03_B,TGAGCTGT,NYU_BMS_Melanoma_13059,yellow_quadrant
80+
AP959450A03,AP959450A03_D12,AP959450A03.D12,C11,D12,NYU_BMS_Melanoma_13059_P1,D12,iTru7_108_12,GGTTCGAG,iTru5_04_B,CGTCAAGA,NYU_BMS_Melanoma_13059,yellow_quadrant
81+
SP464350A04,SP464350A04_D14,SP464350A04.D14,C13,D14,NYU_BMS_Melanoma_13059_P1,D14,iTru7_109_01,GTCGTCTT,iTru5_05_B,AAGCATCG,NYU_BMS_Melanoma_13059,yellow_quadrant
82+
EP121011B01,EP121011B01_D16,EP121011B01.D16,C15,D16,NYU_BMS_Melanoma_13059_P1,D16,iTru7_109_04,GCGGTTAC,iTru5_08_B,ACCTCTTC,NYU_BMS_Melanoma_13059,yellow_quadrant
83+
,,,,,,,,,,,,
84+
[Bioinformatics],,,,,,,,,,,,
85+
Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,contains_replicates,,,,
86+
Feist_11661,11661,FALSE,AACC,GGTT,FALSE,Nextera,Equipment,TRUE,,,,
87+
NYU_BMS_Melanoma_13059,13059,FALSE,AACC,GGTT,FALSE,Knight Lab Kapa HP,Equipment,TRUE,,,,
88+
TMI_10317,10317,FALSE,AACC,GGTT,FALSE,Knight Lab Kapa HP,Eqiiperiment,TRUE,,,,
89+
Other_11223,11223,FALSE,AACC,GGTT,FALSE,Knight Lab Kapa HP,Eqiiperiment,TRUE,,,,
90+
,,,,,,,,,,,,
91+
[Contact],,,,,,,,,,,,
92+
Email,Sample_Project,,,,,,,,,,,
93+
[email protected],Feist_11661,,,,,,,,,,,
94+
[email protected],NYU_BMS_Melanoma_13059,,,,,,,,,,,
95+
,,,,,,,,,,,,
96+
[SampleContext],,,,,,,,,,,,
97+
sample_name,sample_type,primary_qiita_study,secondary_qiita_studies,,,,,,,,,
98+
BLANK.43.12G.A1,control blank,11661,10317;11223,,,,,,,,,
99+
BLANK.43.12H.A3,control blank,11661,10317,,,,,,,,,
100+
BLANK.43.12G.A2,control blank,11661,10317;11223,,,,,,,,,
101+
BLANK.43.12H.A4,control blank,11661,10317,,,,,,,,,
102+
BLANK.43.12G.B2,control blank,11661,10317;11223,,,,,,,,,
103+
BLANK.43.12H.B4,control blank,11661,10317,,,,,,,,,

‎tests/data/good_sheet_w_replicates_and_context_demux_1.csv

Lines changed: 60 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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1+
[Header],,,,,,,,,,,
2+
IEMFileVersion,4,,,,,,,,,,
3+
SheetType,standard_metag,,,,,,,,,,
4+
SheetVersion,101,,,,,,,,,,
5+
Investigator Name,Knight,,,,,,,,,,
6+
Experiment Name,RKL0042,,,,,,,,,,
7+
Date,2/26/20,,,,,,,,,,
8+
Workflow,GenerateFASTQ,,,,,,,,,,
9+
Application,FASTQ Only,,,,,,,,,,
10+
Assay,Metagenomic,,,,,,,,,,
11+
Description,,,,,,,,,,,
12+
Chemistry,Default,,,,,,,,,,
13+
,,,,,,,,,,,
14+
[Reads],,,,,,,,,,,
15+
150,,,,,,,,,,,
16+
150,,,,,,,,,,,
17+
,,,,,,,,,,,
18+
[Settings],,,,,,,,,,,
19+
ReverseComplement,0,,,,,,,,,,
20+
,,,,,,,,,,,
21+
[Data],,,,,,,,,,,
22+
Sample_ID,Sample_Name,well_id_384,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,destination_well_384,sample_plate,source_well_384,well_description
23+
BLANK_43_12G_A1,BLANK.43.12G,A1,iTru7_114_08,CCGACTAT,iTru5_01_A,AAGGCTGA,Feist_11661,A1,Feist_11661_P43,A1,blue_quadrant
24+
RMA_KHP_rpoS_Mage_Q97E_A11,RMA.KHP.rpoS.Mage.Q97E,A11,iTru7_201_01,AACACCAC,iTru5_06_A,CATCTGCT,Feist_11661,A11,Feist_11661_P43,A11,blue_quadrant
25+
JBI_KHP_HGL_021_A13,JBI.KHP.HGL.021,A13,iTru7_201_02,AACTTGCC,iTru5_07_A,GAAGGTTC,Feist_11661,A13,Feist_11661_P43,A13,blue_quadrant
26+
JBI_KHP_HGL_022_A15,JBI.KHP.HGL.022,A15,iTru7_201_03,CGTATCTC,iTru5_08_A,CTCTCAGA,Feist_11661,A15,Feist_11661_P43,A15,blue_quadrant
27+
JBI_KHP_HGL_023_A17,JBI.KHP.HGL.023,A17,iTru7_201_04,CAATGTGG,iTru5_09_A,GAAGAGGT,Feist_11661,A17,Feist_11661_P43,A17,blue_quadrant
28+
JBI_KHP_HGL_024_A19,JBI.KHP.HGL.024,A19,iTru7_201_05,GGTACGAA,iTru5_10_A,TCGTCTGA,Feist_11661,A19,Feist_11661_P43,A19,blue_quadrant
29+
AP581451B02_A21,AP581451B02,A21,iTru7_108_05,TCTGAGAG,iTru5_09_A,CTCTCAGA,NYU_BMS_Melanoma_13059,A21,NYU_BMS_Melanoma_13059_P1,A21,blue_quadrant
30+
EP256645B01_A23,EP256645B01,A23,iTru7_108_06,ACCGCATA,iTru5_10_A,TCGTCTGA,NYU_BMS_Melanoma_13059,A23,NYU_BMS_Melanoma_13059_P1,A23,blue_quadrant
31+
BLANK_43_12H_A3,BLANK.43.12H,A3,iTru7_114_09,ACCGACAA,iTru5_02_A,CGATCGAT,Feist_11661,A3,Feist_11661_P43,A3,blue_quadrant
32+
TMI_test_1_A5,TMI.test.1,A5,iTru7_114_10,CCGACTAT,iTru5_03_A,TTACCGAG,TMI_10317,A5,Feist_11661_P43,A5,blue_quadrant
33+
Other_test_2_A7,Other.test.2,A7,iTru7_114_11,CTTCGCAA,iTru5_04_A,AAGACACC,Other_11223,A7,Feist_11661_P43,A7,blue_quadrant
34+
RMA_KHP_rpoS_Mage_Q97N_A9,RMA.KHP.rpoS.Mage.Q97N,A9,iTru7_114_12,GCCTTGTT,iTru5_05_A,GTCCTAAG,Feist_11661,A9,Feist_11661_P43,A9,blue_quadrant
35+
EP112567B02_C1,EP112567B02,C1,iTru7_108_07,GAAGTACC,iTru5_11_A,CAATAGCC,NYU_BMS_Melanoma_13059,C1,NYU_BMS_Melanoma_13059_P1,C1,blue_quadrant
36+
AP959450A03_C11,AP959450A03,C11,iTru7_108_12,TGTTCGAG,iTru5_04_B,CGTCAAGA,NYU_BMS_Melanoma_13059,C11,NYU_BMS_Melanoma_13059_P1,C11,blue_quadrant
37+
SP464350A04_C13,SP464350A04,C13,iTru7_109_01,CTCGTCTT,iTru5_05_B,AAGCATCG,NYU_BMS_Melanoma_13059,C13,NYU_BMS_Melanoma_13059_P1,C13,blue_quadrant
38+
EP121011B01_C15,EP121011B01,C15,iTru7_109_04,TCGGTTAC,iTru5_08_B,ACCTCTTC,NYU_BMS_Melanoma_13059,C15,NYU_BMS_Melanoma_13059_P1,C15,blue_quadrant
39+
EP337425B01_C3,EP337425B01,C3,iTru7_108_08,CAGGTATC,iTru5_12_A,CATTCGTC,NYU_BMS_Melanoma_13059,C3,NYU_BMS_Melanoma_13059_P1,C3,blue_quadrant
40+
LP127890A01_C5,LP127890A01,C5,iTru7_108_09,TCTCTAGG,iTru5_01_B,AGTGGCAA,NYU_BMS_Melanoma_13059,C5,NYU_BMS_Melanoma_13059_P1,C5,blue_quadrant
41+
EP159692B04_C7,EP159692B04,C7,iTru7_108_10,AAGCACTG,iTru5_02_B,GTGGTATG,NYU_BMS_Melanoma_13059,C7,NYU_BMS_Melanoma_13059_P1,C7,blue_quadrant
42+
EP987683A01_C9,EP987683A01,C9,iTru7_108_11,CCAAGCAA,iTru5_03_B,TGAGCTGT,NYU_BMS_Melanoma_13059,C9,NYU_BMS_Melanoma_13059_P1,C9,blue_quadrant
43+
,,,,,,,,,,,
44+
[Bioinformatics],,,,,,,,,,,
45+
Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,,,,
46+
Feist_11661,11661,False,AACC,GGTT,False,Nextera,Equipment,,,,
47+
NYU_BMS_Melanoma_13059,13059,False,AACC,GGTT,False,Knight Lab Kapa HP,Equipment,,,,
48+
TMI_10317,10317,False,AACC,GGTT,False,Knight Lab Kapa HP,Eqiiperiment,,,,
49+
Other_11223,11223,False,AACC,GGTT,False,Knight Lab Kapa HP,Eqiiperiment,,,,
50+
,,,,,,,,,,,
51+
[Contact],,,,,,,,,,,
52+
Email,Sample_Project,,,,,,,,,,
53+
[email protected],Feist_11661,,,,,,,,,,
54+
[email protected],NYU_BMS_Melanoma_13059,,,,,,,,,,
55+
,,,,,,,,,,,
56+
[SampleContext],,,,,,,,,,,
57+
sample_name,sample_type,primary_qiita_study,secondary_qiita_studies,,,,,,,,
58+
BLANK.43.12G,control blank,11661,10317;11223,,,,,,,,
59+
BLANK.43.12H,control blank,11661,10317,,,,,,,,
60+
,,,,,,,,,,,

‎tests/data/good_sheet_w_replicates_and_context_demux_2.csv

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,60 @@
1+
[Header],,,,,,,,,,,
2+
IEMFileVersion,4,,,,,,,,,,
3+
SheetType,standard_metag,,,,,,,,,,
4+
SheetVersion,101,,,,,,,,,,
5+
Investigator Name,Knight,,,,,,,,,,
6+
Experiment Name,RKL0042,,,,,,,,,,
7+
Date,2/26/20,,,,,,,,,,
8+
Workflow,GenerateFASTQ,,,,,,,,,,
9+
Application,FASTQ Only,,,,,,,,,,
10+
Assay,Metagenomic,,,,,,,,,,
11+
Description,,,,,,,,,,,
12+
Chemistry,Default,,,,,,,,,,
13+
,,,,,,,,,,,
14+
[Reads],,,,,,,,,,,
15+
150,,,,,,,,,,,
16+
150,,,,,,,,,,,
17+
,,,,,,,,,,,
18+
[Settings],,,,,,,,,,,
19+
ReverseComplement,0,,,,,,,,,,
20+
,,,,,,,,,,,
21+
[Data],,,,,,,,,,,
22+
Sample_ID,Sample_Name,well_id_384,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,destination_well_384,sample_plate,source_well_384,well_description
23+
RMA_KHP_rpoS_Mage_Q97N_A10,RMA.KHP.rpoS.Mage.Q97N,A10,iTru7_114_12,GAAGTACC,iTru5_05_A,TGTTCGAG,Feist_11661,A10,Feist_11661_P43,A9,green_quadrant
24+
RMA_KHP_rpoS_Mage_Q97E_A12,RMA.KHP.rpoS.Mage.Q97E,A12,iTru7_201_01,AGTGGCAA,iTru5_06_A,TACTCCAG,Feist_11661,A12,Feist_11661_P43,A11,green_quadrant
25+
JBI_KHP_HGL_021_A14,JBI.KHP.HGL.021,A14,iTru7_201_02,CAGGAATC,iTru5_07_A,CTCGTCTT,Feist_11661,A14,Feist_11661_P43,A13,green_quadrant
26+
JBI_KHP_HGL_022_A16,JBI.KHP.HGL.022,A16,iTru7_201_03,GTGGAATG,iTru5_08_A,GATACCTG,Feist_11661,A16,Feist_11661_P43,A15,green_quadrant
27+
JBI_KHP_HGL_023_A18,JBI.KHP.HGL.023,A18,iTru7_201_04,TCTCAAGG,iTru5_09_A,CGAACTGT,Feist_11661,A18,Feist_11661_P43,A17,green_quadrant
28+
BLANK_43_12G_A2,BLANK.43.12G,A2,iTru7_114_08,TCTGAGAG,iTru5_01_A,AAGCACTG,Feist_11661,A2,Feist_11661_P43,A1,green_quadrant
29+
JBI_KHP_HGL_024_A20,JBI.KHP.HGL.024,A20,iTru7_201_05,TGAGATGT,iTru5_10_A,ACCTCTTC,Feist_11661,A20,Feist_11661_P43,A19,green_quadrant
30+
AP581451B02_A22,AP581451B02,A22,iTru7_108_05,TCTGAAAG,iTru5_09_A,ATCTCAGA,NYU_BMS_Melanoma_13059,A22,NYU_BMS_Melanoma_13059_P1,A21,green_quadrant
31+
EP256645B01_A24,EP256645B01,A24,iTru7_108_06,ACAGCATA,iTru5_10_A,TGGTCTGA,NYU_BMS_Melanoma_13059,A24,NYU_BMS_Melanoma_13059_P1,A23,green_quadrant
32+
BLANK_43_12H_A4,BLANK.43.12H,A4,iTru7_114_09,CAATAGCC,iTru5_02_A,CGTCAAGA,Feist_11661,A4,Feist_11661_P43,A3,green_quadrant
33+
TMI_test_1_A6,TMI.test.1,A6,iTru7_114_10,ACCGCATA,iTru5_03_A,CCAAGCAA,TMI_10317,A6,Feist_11661_P43,A5,green_quadrant
34+
Other_test_2_A8,Other.test.2,A8,iTru7_114_11,CATTCGTC,iTru5_04_A,AAGCATCG,Other_11223,A8,Feist_11661_P43,A7,green_quadrant
35+
EP987683A01_C10,EP987683A01,C10,iTru7_108_11,ACAAGCAA,iTru5_03_B,TGAGCTGT,NYU_BMS_Melanoma_13059,C10,NYU_BMS_Melanoma_13059_P1,C9,green_quadrant
36+
AP959450A03_C12,AP959450A03,C12,iTru7_108_12,AGTTCGAG,iTru5_04_B,CGTCCAGA,NYU_BMS_Melanoma_13059,C12,NYU_BMS_Melanoma_13059_P1,C11,green_quadrant
37+
SP464350A04_C14,SP464350A04,C14,iTru7_109_01,ATCGTCTT,iTru5_05_B,AAGAATCG,NYU_BMS_Melanoma_13059,C14,NYU_BMS_Melanoma_13059_P1,C13,green_quadrant
38+
EP121011B01_C16,EP121011B01,C16,iTru7_109_04,ACGGTTAC,iTru5_08_B,ACCACTTC,NYU_BMS_Melanoma_13059,C16,NYU_BMS_Melanoma_13059_P1,C15,green_quadrant
39+
EP112567B02_C2,EP112567B02,C2,iTru7_108_07,GAAATACC,iTru5_11_A,CATTAGCC,NYU_BMS_Melanoma_13059,C2,NYU_BMS_Melanoma_13059_P1,C1,green_quadrant
40+
EP337425B01_C4,EP337425B01,C4,iTru7_108_08,CAGATATC,iTru5_12_A,CAGTCGTC,NYU_BMS_Melanoma_13059,C4,NYU_BMS_Melanoma_13059_P1,C3,green_quadrant
41+
LP127890A01_C6,LP127890A01,C6,iTru7_108_09,TCTATAGG,iTru5_01_B,AGTCGCAA,NYU_BMS_Melanoma_13059,C6,NYU_BMS_Melanoma_13059_P1,C5,green_quadrant
42+
EP159692B04_C8,EP159692B04,C8,iTru7_108_10,AAGTTATG,iTru5_02_B,GTGGAATG,NYU_BMS_Melanoma_13059,C8,NYU_BMS_Melanoma_13059_P1,C7,green_quadrant
43+
,,,,,,,,,,,
44+
[Bioinformatics],,,,,,,,,,,
45+
Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,,,,
46+
Feist_11661,11661,False,AACC,GGTT,False,Nextera,Equipment,,,,
47+
NYU_BMS_Melanoma_13059,13059,False,AACC,GGTT,False,Knight Lab Kapa HP,Equipment,,,,
48+
TMI_10317,10317,False,AACC,GGTT,False,Knight Lab Kapa HP,Eqiiperiment,,,,
49+
Other_11223,11223,False,AACC,GGTT,False,Knight Lab Kapa HP,Eqiiperiment,,,,
50+
,,,,,,,,,,,
51+
[Contact],,,,,,,,,,,
52+
Email,Sample_Project,,,,,,,,,,
53+
[email protected],Feist_11661,,,,,,,,,,
54+
[email protected],NYU_BMS_Melanoma_13059,,,,,,,,,,
55+
,,,,,,,,,,,
56+
[SampleContext],,,,,,,,,,,
57+
sample_name,sample_type,primary_qiita_study,secondary_qiita_studies,,,,,,,,
58+
BLANK.43.12G,control blank,11661,10317;11223,,,,,,,,
59+
BLANK.43.12H,control blank,11661,10317,,,,,,,,
60+
,,,,,,,,,,,

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