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Merged
mvcowley merged 5 commits into from
Aug 29, 2025
Merged

Add example of pipeline #42

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a27ea74
feat(demo): create demo from test resources
mvcowley Aug 29, 2025
6fc7c47
docs(demo): add demo documentation to README
mvcowley Aug 29, 2025
0fe4076
docs(demo): add runtime estimation of demo to README
mvcowley Aug 29, 2025
3f0b2ef
docs(install): add install time to README
mvcowley Aug 29, 2025
7e7ae29
docs(readme): add system requirements
mvcowley Aug 29, 2025
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315 changes: 168 additions & 147 deletions README.md
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49 changes: 49 additions & 0 deletions examples/Logs/2025_08_29_alpha__Decombinator_Summary.csv
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Original file line number Diff line number Diff line change
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Property,Value
Directory,/home/mcowley/projects/decombinator/Decombinator/examples
InputFile,_alpha
OutputFile,_alpha
DateFinished,2025_08_29
TimeFinished,13:50:47
TimeTaken(Seconds),0.01

InputArguments:,
species,human
chain,a
extension,n12
tags,extended
dontgzip,False
allowNs,False
orientation,reverse
lenthreshold,130
bc_read,R2
bclength,42

NumberReadsInput,106
NumberReadsDecombined,35
PercentReadsDecombined,0.33

ReadsAssignedUsingHalfTags:,
V1error,0
V2error,1
J1error,0
J2error,0

ReadsFilteredOut:,
AmbiguousBaseCall(DCR),0
AmbiguousBaseCall(Barcode),0
OverlongInterTagSeq,0
ImpossibleDeletions,0
OverlappingTagBoundaries,0

ReadsFailedAssignment:,
MultipleVtagMatches,0
VTagAtEndRead,0
VDeletionsUndetermined,0
FoundV1HalfTagNotV2,7
FoundV2HalfTagNotV1,9
NoVDetected,55
MultipleJTagMatches,0
JDeletionsUndermined,0
FoundJ1HalfTagNotJ2,0
FoundJ2HalfTagNotJ1,0
NoJDetected,0
49 changes: 49 additions & 0 deletions examples/Logs/2025_08_29_beta__Decombinator_Summary.csv
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Original file line number Diff line number Diff line change
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Property,Value
Directory,/home/mcowley/projects/decombinator/Decombinator/examples
InputFile,_beta
OutputFile,_beta
DateFinished,2025_08_29
TimeFinished,13:49:52
TimeTaken(Seconds),0.01

InputArguments:,
species,human
chain,b
extension,n12
tags,extended
dontgzip,False
allowNs,False
orientation,reverse
lenthreshold,130
bc_read,R2
bclength,42

NumberReadsInput,106
NumberReadsDecombined,48
PercentReadsDecombined,0.453

ReadsAssignedUsingHalfTags:,
V1error,1
V2error,1
J1error,0
J2error,0

ReadsFilteredOut:,
AmbiguousBaseCall(DCR),0
AmbiguousBaseCall(Barcode),0
OverlongInterTagSeq,0
ImpossibleDeletions,0
OverlappingTagBoundaries,0

ReadsFailedAssignment:,
MultipleVtagMatches,0
VTagAtEndRead,0
VDeletionsUndetermined,0
FoundV1HalfTagNotV2,1
FoundV2HalfTagNotV1,2
NoVDetected,55
MultipleJTagMatches,0
JDeletionsUndermined,0
FoundJ1HalfTagNotJ2,0
FoundJ2HalfTagNotJ1,0
NoJDetected,0
49 changes: 49 additions & 0 deletions examples/Logs/2025_08_29_beta__Decombinator_Summary2.csv
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Original file line number Diff line number Diff line change
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Property,Value
Directory,/home/mcowley/projects/decombinator/Decombinator/examples
InputFile,_beta
OutputFile,_beta
DateFinished,2025_08_29
TimeFinished,13:50:00
TimeTaken(Seconds),0.01

InputArguments:,
species,human
chain,b
extension,n12
tags,extended
dontgzip,False
allowNs,False
orientation,reverse
lenthreshold,130
bc_read,R2
bclength,42

NumberReadsInput,106
NumberReadsDecombined,48
PercentReadsDecombined,0.453

ReadsAssignedUsingHalfTags:,
V1error,1
V2error,1
J1error,0
J2error,0

ReadsFilteredOut:,
AmbiguousBaseCall(DCR),0
AmbiguousBaseCall(Barcode),0
OverlongInterTagSeq,0
ImpossibleDeletions,0
OverlappingTagBoundaries,0

ReadsFailedAssignment:,
MultipleVtagMatches,0
VTagAtEndRead,0
VDeletionsUndetermined,0
FoundV1HalfTagNotV2,1
FoundV2HalfTagNotV1,2
NoVDetected,55
MultipleJTagMatches,0
JDeletionsUndermined,0
FoundJ1HalfTagNotJ2,0
FoundJ2HalfTagNotJ1,0
NoJDetected,0
49 changes: 49 additions & 0 deletions examples/Logs/2025_08_29_beta__Decombinator_Summary3.csv
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Original file line number Diff line number Diff line change
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Property,Value
Directory,/home/mcowley/projects/decombinator/Decombinator/examples
InputFile,_beta
OutputFile,_beta
DateFinished,2025_08_29
TimeFinished,13:50:54
TimeTaken(Seconds),0.01

InputArguments:,
species,human
chain,b
extension,n12
tags,extended
dontgzip,False
allowNs,False
orientation,reverse
lenthreshold,130
bc_read,R2
bclength,42

NumberReadsInput,106
NumberReadsDecombined,48
PercentReadsDecombined,0.453

ReadsAssignedUsingHalfTags:,
V1error,1
V2error,1
J1error,0
J2error,0

ReadsFilteredOut:,
AmbiguousBaseCall(DCR),0
AmbiguousBaseCall(Barcode),0
OverlongInterTagSeq,0
ImpossibleDeletions,0
OverlappingTagBoundaries,0

ReadsFailedAssignment:,
MultipleVtagMatches,0
VTagAtEndRead,0
VDeletionsUndetermined,0
FoundV1HalfTagNotV2,1
FoundV2HalfTagNotV1,2
NoVDetected,55
MultipleJTagMatches,0
JDeletionsUndermined,0
FoundJ1HalfTagNotJ2,0
FoundJ2HalfTagNotJ1,0
NoJDetected,0
30 changes: 30 additions & 0 deletions examples/Logs/2025_08_29_dcr_TINY_1_alpha_CDR3_Translation_Summary.csv
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Property,Value
Directory,/home/mcowley/projects/decombinator/Decombinator/examples
InputFile,TINY_alpha
OutputFile,TINY_alpha
DateFinished,2025_08_29
TimeFinished,13:50:48

InputArguments:,
species,human
chain,a
tags,extended
dontgzip,False

NumberUniqueDCRsInput,26
NumberUniqueDCRsProductive,25
NumberUniqueDCRsNonProductive,1

FunctionalityOfGermlineGenesUsed,
P_V-F,0
P_V-ORF,0
P_V-P,0
P_J-F,0
P_J-ORF,0
P_J-P,0
NP_V-F,0
NP_V-ORF,0
NP_V-P,0
NP_J-F,0
NP_J-ORF,0
NP_J-P,0
38 changes: 38 additions & 0 deletions examples/Logs/2025_08_29_dcr_TINY_1_alpha_Collapsing_Summary.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
Property,Value
Version,5.0.0.dev0
Directory,/home/mcowley/projects/decombinator/Decombinator/examples
InputFile,TINY_alpha
OutputFile,TINY_alpha
DateFinished,2025_08_29
TimeFinished,13:50:47
TimeTaken(Seconds),0.03

extension,freq
dontgzip,False
allowNs,False
dontcheckinput,False
barcodeduplication,False
minbcQ,20
bcQbelowmin,1
bcthreshold,2
lenthreshold,130
percentlevdist,10
avgQthreshold,30
positionalbarcodes,False
oligo,M13

InputUncollapsedDCRLines,35
UniqueDCRsPassingFilters,26
TotalDCRsPassingFilters,30
PercentDCRPassingFilters(withbarcode),0.857
UniqueDCRsPostCollapsing,26
TotalDCRsPostCollapsing,26
PercentUniqueDCRsKept,1.0
PercentTotalDCRsKept,0.867
AverageInputTCRAbundance,1.154
AverageOutputTCRAbundance,1.0
AverageRNAduplication,1.154

BarcodeFail_ContainedNs,0
BarcodeFail_SpacersNotFound,0
BarcodeFail_LowQuality,5
30 changes: 30 additions & 0 deletions examples/Logs/2025_08_29_dcr_TINY_1_beta_CDR3_Translation_Summary.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
Property,Value
Directory,/home/mcowley/projects/decombinator/Decombinator/examples
InputFile,TINY_beta
OutputFile,TINY_beta
DateFinished,2025_08_29
TimeFinished,13:49:53

InputArguments:,
species,human
chain,b
tags,extended
dontgzip,False

NumberUniqueDCRsInput,36
NumberUniqueDCRsProductive,35
NumberUniqueDCRsNonProductive,1

FunctionalityOfGermlineGenesUsed,
P_V-F,0
P_V-ORF,0
P_V-P,0
P_J-F,0
P_J-ORF,0
P_J-P,0
NP_V-F,0
NP_V-ORF,0
NP_V-P,0
NP_J-F,0
NP_J-ORF,0
NP_J-P,0
30 changes: 30 additions & 0 deletions examples/Logs/2025_08_29_dcr_TINY_1_beta_CDR3_Translation_Summary2.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
Property,Value
Directory,/home/mcowley/projects/decombinator/Decombinator/examples
InputFile,TINY_beta
OutputFile,TINY_beta
DateFinished,2025_08_29
TimeFinished,13:50:00

InputArguments:,
species,human
chain,b
tags,extended
dontgzip,False

NumberUniqueDCRsInput,36
NumberUniqueDCRsProductive,35
NumberUniqueDCRsNonProductive,1

FunctionalityOfGermlineGenesUsed,
P_V-F,0
P_V-ORF,0
P_V-P,0
P_J-F,0
P_J-ORF,0
P_J-P,0
NP_V-F,0
NP_V-ORF,0
NP_V-P,0
NP_J-F,0
NP_J-ORF,0
NP_J-P,0
30 changes: 30 additions & 0 deletions examples/Logs/2025_08_29_dcr_TINY_1_beta_CDR3_Translation_Summary3.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
Property,Value
Directory,/home/mcowley/projects/decombinator/Decombinator/examples
InputFile,TINY_beta
OutputFile,TINY_beta
DateFinished,2025_08_29
TimeFinished,13:50:55

InputArguments:,
species,human
chain,b
tags,extended
dontgzip,False

NumberUniqueDCRsInput,36
NumberUniqueDCRsProductive,35
NumberUniqueDCRsNonProductive,1

FunctionalityOfGermlineGenesUsed,
P_V-F,0
P_V-ORF,0
P_V-P,0
P_J-F,0
P_J-ORF,0
P_J-P,0
NP_V-F,0
NP_V-ORF,0
NP_V-P,0
NP_J-F,0
NP_J-ORF,0
NP_J-P,0
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