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replicates
1 parent 41bd0fd commit 0bdd829

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-1351
lines changed

‎src/qp_klp/StandardMetagenomicWorkflow.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -134,6 +134,7 @@ def __init__(self, **kwargs):
134134
bn = basename(f['filepath']).replace(
135135
'.trimmed.fastq.gz', '.fastq.gz')[:-9].replace(
136136
'.', '_') + '.fastq.gz'
137+
bn = bn.replace('_trimmed_filtered', '').replace('10317_', '')
137138
copyfile(f['filepath'], f'{project_folder}/{bn}')
138139
# we need to determine the FILES_REGEX based on the first file
139140
# if the rest do not match we need to raise an error

‎tests/data/bad-sample-sheet-bool-test.csv‎

Lines changed: 0 additions & 816 deletions
This file was deleted.

‎tests/data/bad-sample-sheet-metagenomics.csv‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ Chemistry,Default,,,,,,,,,,
1919
ReverseComplement,0,,,,,,,,,,
2020
,,,,,,,,,,,
2121
[Data],,,,,,,,,,,
22-
Lane,Sample_ID,Sample_Name,Sample_Plate,well_id_384,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,syndna_pool_number,Well_description
22+
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,syndna_pool_number,Well_description
2323
1,CDPH-SAL__Salmonella__Typhi__MDL-143,CDPH-SAL..Salmonella..Typhi..MDL-143,StudyB_11661_P40,A1,iTru7_107_07,CCGACTAT,iTru5_01_A,ACCGACAA,StudyB_11661,pool1,CDPH-SAL_Salmonella Typhi_MDL-143
2424
1,CDPH-SAL_Salmonella_Typhi_MDL-144,CDPH-SAL.Salmonella.Typhi.MDL-144,StudyB_11661_P40,C1,iTru7_107_08,CCGACTAT,iTru5_02_A,CTTCGCAA,StudyB_11661,pool2,CDPH-SAL_Salmonella Typhi_MDL-144
2525
1,CDPH-SAL_Salmonella_Typhi_MDL-145,CDPH-SAL.Salmonella.Typhi.MDL-145,StudyB_11661_P40,E1,iTru7_107_09,GCCTTGTT,iTru5_03_A,AACACCAC,StudyB_11661,pool1,CDPH-SAL_Salmonella Typhi_MDL-145

‎tests/data/good_sheet_w_replicates.csv‎

Lines changed: 92 additions & 92 deletions
Large diffs are not rendered by default.

‎tests/data/good_sheet_w_replicates_and_context.csv‎

Lines changed: 103 additions & 103 deletions
Large diffs are not rendered by default.

‎tests/data/good_sheet_w_replicates_and_context_demux_1.csv‎

Lines changed: 60 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -1,60 +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-
BLANK_43_12G_A1,BLANK.43.12G,A1,iTru7_114_08,CCGACTAT,iTru5_01_A,AAGGCTGA,ProjectF_11661,A1,ProjectF_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,ProjectF_11661,A11,ProjectF_11661_P43,A11,blue_quadrant
25-
JBI_KHP_HGL_021_A13,JBI.KHP.HGL.021,A13,iTru7_201_02,AACTTGCC,iTru5_07_A,GAAGGTTC,ProjectF_11661,A13,ProjectF_11661_P43,A13,blue_quadrant
26-
JBI_KHP_HGL_022_A15,JBI.KHP.HGL.022,A15,iTru7_201_03,CGTATCTC,iTru5_08_A,CTCTCAGA,ProjectF_11661,A15,ProjectF_11661_P43,A15,blue_quadrant
27-
JBI_KHP_HGL_023_A17,JBI.KHP.HGL.023,A17,iTru7_201_04,CAATGTGG,iTru5_09_A,GAAGAGGT,ProjectF_11661,A17,ProjectF_11661_P43,A17,blue_quadrant
28-
JBI_KHP_HGL_024_A19,JBI.KHP.HGL.024,A19,iTru7_201_05,GGTACGAA,iTru5_10_A,TCGTCTGA,ProjectF_11661,A19,ProjectF_11661_P43,A19,blue_quadrant
29-
AP581451B02_A21,AP581451B02,A21,iTru7_108_05,TCTGAGAG,iTru5_09_A,CTCTCAGA,ProjectN_13059,A21,ProjectN_13059_P1,A21,blue_quadrant
30-
EP256645B01_A23,EP256645B01,A23,iTru7_108_06,ACCGCATA,iTru5_10_A,TCGTCTGA,ProjectN_13059,A23,ProjectN_13059_P1,A23,blue_quadrant
31-
BLANK_43_12H_A3,BLANK.43.12H,A3,iTru7_114_09,ACCGACAA,iTru5_02_A,CGATCGAT,ProjectF_11661,A3,ProjectF_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,ProjectF_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,ProjectF_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,ProjectF_11661,A9,ProjectF_11661_P43,A9,blue_quadrant
35-
EP112567B02_C1,EP112567B02,C1,iTru7_108_07,GAAGTACC,iTru5_11_A,CAATAGCC,ProjectN_13059,C1,ProjectN_13059_P1,C1,blue_quadrant
36-
AP959450A03_C11,AP959450A03,C11,iTru7_108_12,TGTTCGAG,iTru5_04_B,CGTCAAGA,ProjectN_13059,C11,ProjectN_13059_P1,C11,blue_quadrant
37-
SP464350A04_C13,SP464350A04,C13,iTru7_109_01,CTCGTCTT,iTru5_05_B,AAGCATCG,ProjectN_13059,C13,ProjectN_13059_P1,C13,blue_quadrant
38-
EP121011B01_C15,EP121011B01,C15,iTru7_109_04,TCGGTTAC,iTru5_08_B,ACCTCTTC,ProjectN_13059,C15,ProjectN_13059_P1,C15,blue_quadrant
39-
EP337425B01_C3,EP337425B01,C3,iTru7_108_08,CAGGTATC,iTru5_12_A,CATTCGTC,ProjectN_13059,C3,ProjectN_13059_P1,C3,blue_quadrant
40-
LP127890A01_C5,LP127890A01,C5,iTru7_108_09,TCTCTAGG,iTru5_01_B,AGTGGCAA,ProjectN_13059,C5,ProjectN_13059_P1,C5,blue_quadrant
41-
EP159692B04_C7,EP159692B04,C7,iTru7_108_10,AAGCACTG,iTru5_02_B,GTGGTATG,ProjectN_13059,C7,ProjectN_13059_P1,C7,blue_quadrant
42-
EP987683A01_C9,EP987683A01,C9,iTru7_108_11,CCAAGCAA,iTru5_03_B,TGAGCTGT,ProjectN_13059,C9,ProjectN_13059_P1,C9,blue_quadrant
43-
,,,,,,,,,,,
44-
[Bioinformatics],,,,,,,,,,,
45-
Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,,,,
46-
ProjectF_11661,11661,False,AACC,GGTT,False,Nextera,Equipment,,,,
47-
ProjectN_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],ProjectF_11661,,,,,,,,,,
54-
[email protected],ProjectN_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-
,,,,,,,,,,,
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,contains_replicates
23+
BLANK_43_12G_A1,BLANK.43.12G,A1,iTru7_114_08,CCGACTAT,iTru5_01_A,AAGGCTGA,ProjectF_11661,A1,ProjectF_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,ProjectF_11661,A11,ProjectF_11661_P43,A11,blue_quadrant,
25+
JBI_KHP_HGL_021_A13,JBI.KHP.HGL.021,A13,iTru7_201_02,AACTTGCC,iTru5_07_A,GAAGGTTC,ProjectF_11661,A13,ProjectF_11661_P43,A13,blue_quadrant,
26+
JBI_KHP_HGL_022_A15,JBI.KHP.HGL.022,A15,iTru7_201_03,CGTATCTC,iTru5_08_A,CTCTCAGA,ProjectF_11661,A15,ProjectF_11661_P43,A15,blue_quadrant,
27+
JBI_KHP_HGL_023_A17,JBI.KHP.HGL.023,A17,iTru7_201_04,CAATGTGG,iTru5_09_A,GAAGAGGT,ProjectF_11661,A17,ProjectF_11661_P43,A17,blue_quadrant,
28+
JBI_KHP_HGL_024_A19,JBI.KHP.HGL.024,A19,iTru7_201_05,GGTACGAA,iTru5_10_A,TCGTCTGA,ProjectF_11661,A19,ProjectF_11661_P43,A19,blue_quadrant,
29+
AP581451B02_A21,AP581451B02,A21,iTru7_108_05,TCTGAGAG,iTru5_09_A,CTCTCAGA,ProjectN_13059,A21,ProjectN_13059_P1,A21,blue_quadrant,
30+
EP256645B01_A23,EP256645B01,A23,iTru7_108_06,ACCGCATA,iTru5_10_A,TCGTCTGA,ProjectN_13059,A23,ProjectN_13059_P1,A23,blue_quadrant,
31+
BLANK_43_12H_A3,BLANK.43.12H,A3,iTru7_114_09,ACCGACAA,iTru5_02_A,CGATCGAT,ProjectF_11661,A3,ProjectF_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,ProjectF_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,ProjectF_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,ProjectF_11661,A9,ProjectF_11661_P43,A9,blue_quadrant,
35+
EP112567B02_C1,EP112567B02,C1,iTru7_108_07,GAAGTACC,iTru5_11_A,CAATAGCC,ProjectN_13059,C1,ProjectN_13059_P1,C1,blue_quadrant,
36+
AP959450A03_C11,AP959450A03,C11,iTru7_108_12,TGTTCGAG,iTru5_04_B,CGTCAAGA,ProjectN_13059,C11,ProjectN_13059_P1,C11,blue_quadrant,
37+
SP464350A04_C13,SP464350A04,C13,iTru7_109_01,CTCGTCTT,iTru5_05_B,AAGCATCG,ProjectN_13059,C13,ProjectN_13059_P1,C13,blue_quadrant,
38+
EP121011B01_C15,EP121011B01,C15,iTru7_109_04,TCGGTTAC,iTru5_08_B,ACCTCTTC,ProjectN_13059,C15,ProjectN_13059_P1,C15,blue_quadrant,
39+
EP337425B01_C3,EP337425B01,C3,iTru7_108_08,CAGGTATC,iTru5_12_A,CATTCGTC,ProjectN_13059,C3,ProjectN_13059_P1,C3,blue_quadrant,
40+
LP127890A01_C5,LP127890A01,C5,iTru7_108_09,TCTCTAGG,iTru5_01_B,AGTGGCAA,ProjectN_13059,C5,ProjectN_13059_P1,C5,blue_quadrant,
41+
EP159692B04_C7,EP159692B04,C7,iTru7_108_10,AAGCACTG,iTru5_02_B,GTGGTATG,ProjectN_13059,C7,ProjectN_13059_P1,C7,blue_quadrant,
42+
EP987683A01_C9,EP987683A01,C9,iTru7_108_11,CCAAGCAA,iTru5_03_B,TGAGCTGT,ProjectN_13059,C9,ProjectN_13059_P1,C9,blue_quadrant,
43+
,,,,,,,,,,,,
44+
[Bioinformatics],,,,,,,,,,,,
45+
Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,,,,,
46+
ProjectF_11661,11661,False,AACC,GGTT,False,Nextera,Equipment,,,,,
47+
ProjectN_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],ProjectF_11661,,,,,,,,,,,
54+
[email protected],ProjectN_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

Lines changed: 60 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -1,60 +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,ProjectF_11661,A10,ProjectF_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,ProjectF_11661,A12,ProjectF_11661_P43,A11,green_quadrant
25-
JBI_KHP_HGL_021_A14,JBI.KHP.HGL.021,A14,iTru7_201_02,CAGGAATC,iTru5_07_A,CTCGTCTT,ProjectF_11661,A14,ProjectF_11661_P43,A13,green_quadrant
26-
JBI_KHP_HGL_022_A16,JBI.KHP.HGL.022,A16,iTru7_201_03,GTGGAATG,iTru5_08_A,GATACCTG,ProjectF_11661,A16,ProjectF_11661_P43,A15,green_quadrant
27-
JBI_KHP_HGL_023_A18,JBI.KHP.HGL.023,A18,iTru7_201_04,TCTCAAGG,iTru5_09_A,CGAACTGT,ProjectF_11661,A18,ProjectF_11661_P43,A17,green_quadrant
28-
BLANK_43_12G_A2,BLANK.43.12G,A2,iTru7_114_08,TCTGAGAG,iTru5_01_A,AAGCACTG,ProjectF_11661,A2,ProjectF_11661_P43,A1,green_quadrant
29-
JBI_KHP_HGL_024_A20,JBI.KHP.HGL.024,A20,iTru7_201_05,TGAGATGT,iTru5_10_A,ACCTCTTC,ProjectF_11661,A20,ProjectF_11661_P43,A19,green_quadrant
30-
AP581451B02_A22,AP581451B02,A22,iTru7_108_05,TCTGAAAG,iTru5_09_A,ATCTCAGA,ProjectN_13059,A22,ProjectN_13059_P1,A21,green_quadrant
31-
EP256645B01_A24,EP256645B01,A24,iTru7_108_06,ACAGCATA,iTru5_10_A,TGGTCTGA,ProjectN_13059,A24,ProjectN_13059_P1,A23,green_quadrant
32-
BLANK_43_12H_A4,BLANK.43.12H,A4,iTru7_114_09,CAATAGCC,iTru5_02_A,CGTCAAGA,ProjectF_11661,A4,ProjectF_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,ProjectF_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,ProjectF_11661_P43,A7,green_quadrant
35-
EP987683A01_C10,EP987683A01,C10,iTru7_108_11,ACAAGCAA,iTru5_03_B,TGAGCTGT,ProjectN_13059,C10,ProjectN_13059_P1,C9,green_quadrant
36-
AP959450A03_C12,AP959450A03,C12,iTru7_108_12,AGTTCGAG,iTru5_04_B,CGTCCAGA,ProjectN_13059,C12,ProjectN_13059_P1,C11,green_quadrant
37-
SP464350A04_C14,SP464350A04,C14,iTru7_109_01,ATCGTCTT,iTru5_05_B,AAGAATCG,ProjectN_13059,C14,ProjectN_13059_P1,C13,green_quadrant
38-
EP121011B01_C16,EP121011B01,C16,iTru7_109_04,ACGGTTAC,iTru5_08_B,ACCACTTC,ProjectN_13059,C16,ProjectN_13059_P1,C15,green_quadrant
39-
EP112567B02_C2,EP112567B02,C2,iTru7_108_07,GAAATACC,iTru5_11_A,CATTAGCC,ProjectN_13059,C2,ProjectN_13059_P1,C1,green_quadrant
40-
EP337425B01_C4,EP337425B01,C4,iTru7_108_08,CAGATATC,iTru5_12_A,CAGTCGTC,ProjectN_13059,C4,ProjectN_13059_P1,C3,green_quadrant
41-
LP127890A01_C6,LP127890A01,C6,iTru7_108_09,TCTATAGG,iTru5_01_B,AGTCGCAA,ProjectN_13059,C6,ProjectN_13059_P1,C5,green_quadrant
42-
EP159692B04_C8,EP159692B04,C8,iTru7_108_10,AAGTTATG,iTru5_02_B,GTGGAATG,ProjectN_13059,C8,ProjectN_13059_P1,C7,green_quadrant
43-
,,,,,,,,,,,
44-
[Bioinformatics],,,,,,,,,,,
45-
Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,,,,
46-
ProjectF_11661,11661,False,AACC,GGTT,False,Nextera,Equipment,,,,
47-
ProjectN_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],ProjectF_11661,,,,,,,,,,
54-
[email protected],ProjectN_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-
,,,,,,,,,,,
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,contains_replicates
23+
RMA_KHP_rpoS_Mage_Q97N_A10,RMA.KHP.rpoS.Mage.Q97N,A10,iTru7_114_12,GAAGTACC,iTru5_05_A,TGTTCGAG,ProjectF_11661,A10,ProjectF_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,ProjectF_11661,A12,ProjectF_11661_P43,A11,green_quadrant,
25+
JBI_KHP_HGL_021_A14,JBI.KHP.HGL.021,A14,iTru7_201_02,CAGGAATC,iTru5_07_A,CTCGTCTT,ProjectF_11661,A14,ProjectF_11661_P43,A13,green_quadrant,
26+
JBI_KHP_HGL_022_A16,JBI.KHP.HGL.022,A16,iTru7_201_03,GTGGAATG,iTru5_08_A,GATACCTG,ProjectF_11661,A16,ProjectF_11661_P43,A15,green_quadrant,
27+
JBI_KHP_HGL_023_A18,JBI.KHP.HGL.023,A18,iTru7_201_04,TCTCAAGG,iTru5_09_A,CGAACTGT,ProjectF_11661,A18,ProjectF_11661_P43,A17,green_quadrant,
28+
BLANK_43_12G_A2,BLANK.43.12G,A2,iTru7_114_08,TCTGAGAG,iTru5_01_A,AAGCACTG,ProjectF_11661,A2,ProjectF_11661_P43,A1,green_quadrant,
29+
JBI_KHP_HGL_024_A20,JBI.KHP.HGL.024,A20,iTru7_201_05,TGAGATGT,iTru5_10_A,ACCTCTTC,ProjectF_11661,A20,ProjectF_11661_P43,A19,green_quadrant,
30+
AP581451B02_A22,AP581451B02,A22,iTru7_108_05,TCTGAAAG,iTru5_09_A,ATCTCAGA,ProjectN_13059,A22,ProjectN_13059_P1,A21,green_quadrant,
31+
EP256645B01_A24,EP256645B01,A24,iTru7_108_06,ACAGCATA,iTru5_10_A,TGGTCTGA,ProjectN_13059,A24,ProjectN_13059_P1,A23,green_quadrant,
32+
BLANK_43_12H_A4,BLANK.43.12H,A4,iTru7_114_09,CAATAGCC,iTru5_02_A,CGTCAAGA,ProjectF_11661,A4,ProjectF_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,ProjectF_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,ProjectF_11661_P43,A7,green_quadrant,
35+
EP987683A01_C10,EP987683A01,C10,iTru7_108_11,ACAAGCAA,iTru5_03_B,TGAGCTGT,ProjectN_13059,C10,ProjectN_13059_P1,C9,green_quadrant,
36+
AP959450A03_C12,AP959450A03,C12,iTru7_108_12,AGTTCGAG,iTru5_04_B,CGTCCAGA,ProjectN_13059,C12,ProjectN_13059_P1,C11,green_quadrant,
37+
SP464350A04_C14,SP464350A04,C14,iTru7_109_01,ATCGTCTT,iTru5_05_B,AAGAATCG,ProjectN_13059,C14,ProjectN_13059_P1,C13,green_quadrant,
38+
EP121011B01_C16,EP121011B01,C16,iTru7_109_04,ACGGTTAC,iTru5_08_B,ACCACTTC,ProjectN_13059,C16,ProjectN_13059_P1,C15,green_quadrant,
39+
EP112567B02_C2,EP112567B02,C2,iTru7_108_07,GAAATACC,iTru5_11_A,CATTAGCC,ProjectN_13059,C2,ProjectN_13059_P1,C1,green_quadrant,
40+
EP337425B01_C4,EP337425B01,C4,iTru7_108_08,CAGATATC,iTru5_12_A,CAGTCGTC,ProjectN_13059,C4,ProjectN_13059_P1,C3,green_quadrant,
41+
LP127890A01_C6,LP127890A01,C6,iTru7_108_09,TCTATAGG,iTru5_01_B,AGTCGCAA,ProjectN_13059,C6,ProjectN_13059_P1,C5,green_quadrant,
42+
EP159692B04_C8,EP159692B04,C8,iTru7_108_10,AAGTTATG,iTru5_02_B,GTGGAATG,ProjectN_13059,C8,ProjectN_13059_P1,C7,green_quadrant,
43+
,,,,,,,,,,,,
44+
[Bioinformatics],,,,,,,,,,,,
45+
Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,,,,,
46+
ProjectF_11661,11661,False,AACC,GGTT,False,Nextera,Equipment,,,,,
47+
ProjectN_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],ProjectF_11661,,,,,,,,,,,
54+
[email protected],ProjectN_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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