THIS REPO IS 🚧 UNDER CONSTRUCTION 🚧 and NOT Used in ANY production CODE
core
flowchart TD
p0((Channel.fromPath))
p1[coreEntry:coreWorkflow:moveUnambiguousAminoAcidSequencesFirst]
p2[coreEntry:coreWorkflow:orthoFinderSetup]
p3(( ))
p4(( ))
p5(( ))
p6[coreEntry:coreWorkflow:mapCachedBlasts]
p7([splitText])
p8([map])
p9([toList])
p10([splitText])
p11([map])
p12([toList])
p13([map])
p14([flatMap])
p15([groupTuple])
p16([collect])
p17([collect])
p18(( ))
p19[coreEntry:coreWorkflow:diamond]
p20([collect])
p21[coreEntry:coreWorkflow:computeGroups]
p22(( ))
p23([flatten])
p24([collect])
p25([collect])
p26([collect])
p27(( ))
p28[coreEntry:coreWorkflow:splitOrthologGroupsPerSpecies]
p29([collect])
p30[coreEntry:coreWorkflow:makeOrthogroupDiamondFiles]
p31([flatten])
p32([collectFile])
p33([collect])
p34([collect])
p35(( ))
p36[coreEntry:coreWorkflow:bestRepresentativesAndStats:makeFullSingletonsFile]
p37([collate])
p38[coreEntry:coreWorkflow:bestRepresentativesAndStats:findBestRepresentatives]
p39([flatten])
p40([collectFile])
p41([concat])
p42[coreEntry:coreWorkflow:bestRepresentativesAndStats:removeEmptyGroups]
p43(( ))
p44[coreEntry:coreWorkflow:bestRepresentativesAndStats:makeBestRepresentativesFasta]
p45([splitText])
p46[coreEntry:coreWorkflow:bestRepresentativesAndStats:filterSimilaritiesByBestRepresentative]
p47([collect])
p48([splitFasta])
p49([flatten])
p50([collate])
p51(( ))
p52(( ))
p53[coreEntry:coreWorkflow:bestRepresentativesAndStats:calculateGroupResults]
p54([collectFile])
p55(( ))
p56[coreEntry:coreWorkflow:bestRepresentativesAndStats:coreBestRepsToCoreDiamond]
p57([collectFile])
p58(( ))
p59[coreEntry:coreWorkflow:bestRepresentativesAndStats:translateSingletonsFile]
p60(( ))
p61[coreEntry:coreWorkflow:bestRepresentativesAndStats:reformatGroupsFile]
p62(( ))
p0 -->|inputFile| p1
p1 --> p2
p2 --> p3
p2 -->|setupOrthofinderWorkingDir| p16
p2 --> p6
p2 -->|setupSequenceMapping| p6
p4 -->|previousDiamondCacheDirectory| p6
p5 -->|outdatedOrganisms| p6
p6 --> p17
p2 --> p7
p7 --> p8
p8 --> p9
p9 -->|speciesIds| p13
p2 --> p10
p10 --> p11
p11 --> p12
p12 -->|speciesNames| p23
p13 --> p14
p14 --> p15
p15 -->|speciesPairsAsTuple| p19
p16 --> p19
p17 --> p19
p18 -->|outputList| p19
p19 --> p20
p20 -->|collectedDiamondResults| p21
p2 -->|setupOrthofinderWorkingDir| p21
p21 -->|orthofinderGroupResultsOrthologgroups| p26
p21 --> p22
p23 --> p28
p2 --> p24
p24 --> p28
p2 -->|setupSequenceMapping| p25
p25 --> p28
p26 --> p28
p27 -->|buildVersion| p28
p28 --> p29
p28 -->|speciesOrthologsSingletons| p34
p29 --> p30
p15 -->|speciesPairsAsTuple| p30
p20 -->|collectedDiamondResults| p30
p30 -->|diamondSimilaritiesPerGroup| p31
p31 --> p32
p32 -->|allDiamondSimilaritiesPerGroup| p33
p33 -->|allDiamondSimilarities| p46
p34 -->|singletonFiles| p36
p21 -->|orthofinderGroupResultsOrthologgroups| p36
p35 -->|buildVersion| p36
p36 --> p41
p32 -->|allDiamondSimilaritiesPerGroup| p37
p37 --> p38
p38 --> p39
p39 --> p40
p40 --> p41
p41 --> p42
p42 --> p44
p2 -->|setupOrthofinderWorkingDir| p44
p43 -->|isResidual| p44
p44 --> p48
p42 --> p45
p45 --> p46
p36 -->|singletons| p46
p46 --> p47
p47 -->|groupResultsOfBestRep| p49
p48 -->|bestRepSubset| p56
p49 --> p50
p50 --> p53
p51 -->|evalueColumn| p53
p52 -->|isResidual| p53
p53 --> p54
p54 --> p55
p44 -->|bestRepsFasta| p56
p56 --> p57
p57 -->|bestRepsSelfDiamondResults| p58
p36 -->|singletonsFile| p59
p2 -->|setupSequenceMapping| p59
p59 --> p61
p21 -->|orthofinderGroupResultsOrthologgroups| p61
p60 -->|buildVersion| p61
p61 --> p62
peripheral
flowchart TD
p0((Channel.fromPath))
p1[peripheralEntry:peripheralWorkflow:uncompressPeripheralFastas]
p2(( ))
p3(( ))
p4[peripheralEntry:peripheralWorkflow:uncompressFastas]
p5(( ))
p6(( ))
p7[peripheralEntry:peripheralWorkflow:createDatabase]
p8(( ))
p9(( ))
p10[peripheralEntry:peripheralWorkflow:cleanPeripheralDiamondCache]
p11([flatten])
p12(( ))
p13[peripheralEntry:peripheralWorkflow:peripheralDiamond]
p14[peripheralEntry:peripheralWorkflow:assignGroups]
p15[peripheralEntry:peripheralWorkflow:makeResidualAndPeripheralFastas]
p16([collectFile])
p17([collectFile])
p18([collectFile])
p19[peripheralEntry:peripheralWorkflow:getPeripheralResultsToBestRep]
p20([flatten])
p21([collectFile])
p22([collect])
p23(( ))
p24[peripheralEntry:peripheralWorkflow:combinePeripheralAndCoreSimilaritiesToBestReps]
p25([collect])
p26(( ))
p27[peripheralEntry:peripheralWorkflow:combineProteomes]
p28(( ))
p29[peripheralEntry:peripheralWorkflow:makeGroupsFile]
p30([splitText])
p31(( ))
p32[peripheralEntry:peripheralWorkflow:splitProteomeByGroup]
p33(( ))
p34[peripheralEntry:peripheralWorkflow:createCompressedFastaDir]
p35(( ))
p36[peripheralEntry:peripheralWorkflow:residualWorkflow:moveUnambiguousAminoAcidSequencesFirst]
p37[peripheralEntry:peripheralWorkflow:residualWorkflow:orthoFinderSetup]
p38(( ))
p39[peripheralEntry:peripheralWorkflow:residualWorkflow:createEmptyDir]
p40([collect])
p41([splitText])
p42([map])
p43([toList])
p44([splitText])
p45([map])
p46([toList])
p47([map])
p48([flatMap])
p49([groupTuple])
p50([collect])
p51([collect])
p52(( ))
p53[peripheralEntry:peripheralWorkflow:residualWorkflow:diamond]
p54([collect])
p55[peripheralEntry:peripheralWorkflow:residualWorkflow:computeGroups]
p56(( ))
p57([flatten])
p58([collect])
p59([collect])
p60([collect])
p61(( ))
p62[peripheralEntry:peripheralWorkflow:residualWorkflow:splitOrthologGroupsPerSpecies]
p63([collect])
p64[peripheralEntry:peripheralWorkflow:residualWorkflow:makeOrthogroupDiamondFiles]
p65([flatten])
p66([collectFile])
p67([collect])
p68([collect])
p69(( ))
p70[peripheralEntry:peripheralWorkflow:residualWorkflow:bestRepresentativesAndStats:makeFullSingletonsFile]
p71([collate])
p72[peripheralEntry:peripheralWorkflow:residualWorkflow:bestRepresentativesAndStats:findBestRepresentatives]
p73([flatten])
p74([collectFile])
p75([concat])
p76[peripheralEntry:peripheralWorkflow:residualWorkflow:bestRepresentativesAndStats:removeEmptyGroups]
p77(( ))
p78[peripheralEntry:peripheralWorkflow:residualWorkflow:bestRepresentativesAndStats:makeBestRepresentativesFasta]
p79([splitText])
p80[peripheralEntry:peripheralWorkflow:residualWorkflow:bestRepresentativesAndStats:filterSimilaritiesByBestRepresentative]
p81([collect])
p82([splitFasta])
p83([flatten])
p84([collate])
p85(( ))
p86(( ))
p87[peripheralEntry:peripheralWorkflow:residualWorkflow:bestRepresentativesAndStats:calculateGroupResults]
p88([collectFile])
p89(( ))
p90(( ))
p91[peripheralEntry:peripheralWorkflow:residualWorkflow:bestRepresentativesAndStats:mergeCoreAndResidualBestReps]
p92[peripheralEntry:peripheralWorkflow:residualWorkflow:bestRepresentativesAndStats:residualBestRepsToCoreAndResidualDiamond]
p93([collectFile])
p94((Channel.fromPath))
p95([splitFasta])
p96[peripheralEntry:peripheralWorkflow:residualWorkflow:bestRepresentativesAndStats:coreBestRepsToResidualDiamond]
p97([collectFile])
p98((Channel.fromPath))
p99([concat])
p100([concat])
p101([collectFile])
p102(( ))
p0 -->|peripheralDir| p1
p1 --> p11
p1 --> p2
p3 -->|inputDir| p4
p4 --> p5
p4 --> p27
p6 -->|newdbfasta| p7
p7 --> p13
p8 -->|outdatedOrganisms| p10
p9 -->|peripheralDiamondCache| p10
p10 --> p13
p11 --> p13
p12 -->|outputList| p13
p13 --> p14
p13 -->|fasta| p14
p14 --> p15
p14 -->|diamondInput| p19
p14 -->|fasta| p15
p15 --> p16
p15 --> p17
p16 -->|residualFasta| p34
p17 -->|peripheralFasta| p27
p14 --> p18
p18 -->|groupAssignments| p29
p14 -->|groupAssignments| p19
p19 --> p20
p20 --> p21
p21 --> p22
p22 -->|peripheralSimilaritiesToBestRep| p24
p23 -->|coreGroupSimilarities| p24
p24 --> p25
p25 -->|allSimilaritiesToBestRep| p26
p27 --> p32
p28 -->|coreGroups| p29
p29 --> p30
p30 --> p32
p31 -->|outdated| p32
p32 --> p33
p34 -->|inputFile| p36
p34 -->|-| p35
p36 --> p37
p37 --> p38
p37 -->|setupOrthofinderWorkingDir| p50
p37 --> p39
p37 -->|setupSequenceMapping| p59
p39 --> p40
p40 -->|mappedCachedBlasts| p51
p37 --> p41
p41 --> p42
p42 --> p43
p43 -->|speciesIds| p47
p37 --> p44
p44 --> p45
p45 --> p46
p46 -->|speciesNames| p57
p47 --> p48
p48 --> p49
p49 -->|speciesPairsAsTuple| p53
p50 --> p53
p51 --> p53
p52 -->|outputList| p53
p53 --> p54
p54 -->|collectedDiamondResults| p55
p37 -->|setupOrthofinderWorkingDir| p55
p55 -->|orthofinderGroupResultsOrthologgroups| p60
p55 --> p56
p57 --> p62
p37 --> p58
p58 --> p62
p59 --> p62
p60 --> p62
p61 -->|buildVersion| p62
p62 --> p63
p62 -->|speciesOrthologsSingletons| p68
p63 --> p64
p49 -->|speciesPairsAsTuple| p64
p54 -->|collectedDiamondResults| p64
p64 -->|diamondSimilaritiesPerGroup| p65
p65 --> p66
p66 -->|allDiamondSimilaritiesPerGroup| p67
p67 -->|allDiamondSimilarities| p80
p68 -->|singletonFiles| p70
p55 -->|orthofinderGroupResultsOrthologgroups| p70
p69 -->|buildVersion| p70
p70 --> p75
p66 -->|allDiamondSimilaritiesPerGroup| p71
p71 --> p72
p72 --> p73
p73 --> p74
p74 --> p75
p75 --> p76
p76 --> p78
p37 -->|setupOrthofinderWorkingDir| p78
p77 -->|isResidual| p78
p78 --> p82
p76 --> p79
p79 --> p80
p70 -->|singletons| p80
p80 --> p81
p81 -->|groupResultsOfBestRep| p83
p82 -->|bestRepSubset| p92
p83 --> p84
p84 --> p87
p85 -->|evalueColumn| p87
p86 -->|isResidual| p87
p87 --> p88
p88 --> p89
p78 -->|residualBestReps| p91
p90 -->|coreBestReps.fasta| p91
p91 --> p92
p92 --> p93
p93 -->|residualBestRepsSimilarities| p99
p94 -->|coreBestRepsFasta| p95
p95 -->|coreBestRepsFastaSubset| p96
p78 -->|bestRepsFasta| p96
p96 --> p97
p97 -->|coreToResidualBestRepsSimilarities| p100
p98 --> p99
p99 --> p100
p100 --> p101
p101 --> p102
Explanation of Config File Parameters
| core | peripheral | Parameter | Value | Description |
|---|---|---|---|---|
| X | X | outputDir | string path | Where you would like the output files to be stored |
| X | X | outdatedOrganisms | string path | Path to the file containing outdated organisms abbrevs (generated with checkForUpdate workflow) |
| X | X | buildVersion | string | Build version number |
| X | orthoFinderDiamondOutputFields | string | String of outputs passed to diamond job. This should NOT be changed | |
| X | bestRepDiamondOutputFields | string | String of outputs passed to diamond job. This should NOT be changed | |
| X | proteomes | string path | Compressed directory of core organism fasta files | |
| X | diamondSimilarityCache | string path | Path to cache directory of diamond similarity results for the core | |
| X | coreProteomes | string path | Path to the input directory of core proteomes | |
| X | coreBestReps | string path | Path to the best representative file produced by the core workflow | |
| X | peripheralProteomes | string path | Path to peripheral proteomes | |
| X | coreGroupsFile | string path | Path to groups file output by core workflow | |
| X | peripheralDiamondCache | string path | Path to peripheral diamond similarity cache of peripheral to core best rep jobs | |
| X | coreSimilarityToBestReps | string path | Path to the group similarity results produced by the core workflow | |
| X | coreBestRepsSelfBlast | string path | Path to core output file indicating the which groups are similar |