-----------------------------------------------------------------------------------------------
                                |                      S   T   A   G   E                      |
                                ---------------------------------------------------------------
                                |          c                                 c                |
                                |          r                        j   g    o                |
                                |          e                        o   e    m                |
                                |          a                        i   n    b                |
                                |          t                        n   e c  G                |
                                | c        e                     j  t   r o  e                |
                                | o        L                     o  F   a m  n                |
                                | n        i      i              i  i   t b  e                |
                                | v        s f i  m              n  l   e i  r                |
                                | e        t i m  p              t  t g Q n  a                |
                                | r c      O l p  u        c m   C  e e Q e  t                |
                                | t r      f t u  t        o e   o  r n M P  e p              |
                                | F e      E e t  e f      l r   n  e e a a  M h              |
                                | r a      x r e  W i      l g f d  d r n n  a e              |
                                | o t p    c H W  i l      e e i e  B a h e  n n              |
                                | m e h    l a i  t t      c T l n  y t a l  h o              |
wfRequiredDeep                  | B R a    u p t  h e      t w t s  A e t s  a A              |
                                | e s s  p d l h  M r q s  S o e e  l T a C  t n              |
Matrix of Stages when           | d I i  h e o I  i B c n  u C r d  l o n o  t a              |
IMPUTE tool is used             | T d n  a d t m  n y t p  m h B F  F p P m  a l u v  w x y z |
                                | o L g  s S y p  i I o t  m u y i  i H l p  n y t t  t t t t |
                                | B i B  i n p u  m n o e  a n A l  l i o l  T s a a  a a a a |
                                | e s e  n p e t  a f l s  r k l e  e t t e  o i s s  s s s s |
                                | d t d  g s s e  c o S t  y s l s  s s s x  p s k k  k k k k |
---------------------------------------- --------- --------------------------------------------
until_convertFromBedToBed       | 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x6000000
until_phasing                   | 1 1 1  1 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x7800000
until_imputation                | 1 1 1  1 0 0 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x7900000
until_qctools                   | 1 1 1  1 0 0 1  0 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x7960000
until_association               | 1 1 1  1 0 0 1  0 1 1 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x7970000
until_filterByAll               | 1 1 1  1 0 0 1  0 1 1 1  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x797E000 
until_summary                   | 1 1 1  1 0 0 1  0 1 1 1  1 1 1 1  1 1 1 1  1 0 0 0  0 0 0 0 | 0x797FF80
whole_workflow                  | 1 1 1  1 0 0 1  0 1 1 1  1 1 1 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x797FFC0 
from_phasing                    | 0 0 0  0 0 0 1  0 1 1 1  1 1 1 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x017FFC0
from_phasing_to_summary         | 0 0 0  0 0 0 1  0 1 1 1  1 1 1 1  1 1 1 1  1 0 0 0  0 0 0 0 | 0x017FF80
from_phasing_to_filterByAll     | 0 0 0  0 0 0 1  0 1 1 1  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x017E000
from_phasing_to_association	    | 0 0 0  0 0 0 1  0 1 1 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0170000
from_phasing_to_qctools         | 0 0 0  0 0 0 1  0 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0160000
from_phasing_to_imputation	    | 0 0 0  0 0 0 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0100000
from_imputation                 | 0 0 0  0 0 0 0  0 1 1 1  1 1 1 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x007FFC0
from_imputation_to_summary	    | 0 0 0  0 0 0 0  0 1 1 1  1 1 1 1  1 1 1 1  0 0 0 0  0 0 0 0 | 0x007FF00
from_imputation_to_filterByAll  | 0 0 0  0 0 0 0  0 1 1 1  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x007E000
from_imputation_to_association	| 0 0 0  0 0 0 0  0 1 1 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0070000
from_imputation_to_filterByInfo | 0 0 0  0 0 0 0  0 1 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0040000
from_filterByInfo_to_qctoolS    | 0 0 0  0 0 0 0  0 0 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0020000
from_qctoolS_to_association     | 0 0 0  0 0 0 0  0 0 0 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0010000
from_association                | 0 0 0  0 0 0 0  0 0 0 0  1 1 1 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x000FFC0
from_association_to_filterByAll | 0 0 0  0 0 0 0  0 0 0 0  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x000E000
from_association_to_summary	    | 0 0 0  0 0 0 0  0 0 0 0  1 1 1 1  1 1 1 1  1 0 0 0  0 0 0 0 | 0x000FF80
from_filterByAll                | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x0001FC0
from_jointFiltered_to_condensed | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  1 0 0 0  0 0 0 0  0 0 0 0 | 0x0000800
from_filterByAll_to_summary     | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  1 1 1 1  1 0 0 0  0 0 0 0 | 0x0001F80
from_manhattan_to_combine       | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  0 0 1 0  0 0 0 0  0 0 0 0 | 0x0001200
from_combine_to_manhattan       | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  0 0 0 0  0 0 0 0 | 0x0000100
from_combine_to_summary         | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  1 0 0 0  0 0 0 0 | 0x0000180
from_combine                    | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  1 1 0 0  0 0 0 0 | 0x00001C0
from_combineGenManTop_to_summary| 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  1 0 0 0  0 0 0 0 | 0x0000080
from_summary                    | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 1 0 0  0 0 0 0 | 0x0000040
-----------------------------------------------------------------------------------------------


-----------------------------------------------------------------------------------------------
                                |                      S   T   A   G   E                      |
                                ---------------------------------------------------------------
                                |          c                                 c                |
                                |          r                        j   g    o                |
                                |          e                        o   e    m                |
                                |          a                        i   n    b                |
                                |          t                        n   e c  G                |
                                | c        e                     j  t   r o  e                |
                                | o        L                     o  F   a m  n                |
                                | n        i      i              i  i   t b  e                |
                                | v        s f i  m              n  l   e i  r                |
                                | e        t i m  p              t  t g Q n  a                |
                                | r c      O l p  u        c m   C  e e Q e  t                |
                                | t r      f t u  t        o e   o  r n M P  e p              |
                                | F e      E e t  e f      l r   n  e e a a  M h              |
                                | r a      x r e  W i      l g f d  d r n n  a e              |
                                | o t p    c H W  i l      e e i e  B a h e  n n              |
                                | m e h    l a i  t t      c T l n  y t a l  h o              |
wfRequiredDeep                  | B R a    u p t  h e      t w t s  A e t s  a A              |
                                | e s s  p d l h  M r q s  S o e e  l T a C  t n              |
Matrix of Stages when           | d I i  h e o I  i B c n  u C r d  l o n o  t a              |
Minimac3 tool is used           | T d n  a d t m  n y t p  m h B F  F p P m  a l u v  w x y z |
                                | o L g  s S y p  i I o t  m u y i  i H l p  n y t t  t t t t |
                                | B i B  i n p u  m n o e  a n A l  l i o l  T s a a  a a a a |
                                | e s e  n p e t  a f l s  r k l e  e t t e  o i s s  s s s s |
                                | d t d  g s s e  c o S t  y s l s  s s s x  p s k k  k k k k |
------------------------------------------ ----- --- ------------------------------------------
until_convertFromBedToBed       | 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x6000000
until_phasing                   | 1 1 1  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x7E00000
until_imputation                | 1 1 1  1 1 1 0  1 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x7E80000
until_qctools                   | 1 1 1  1 1 1 0  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x7EE0000
until_association               | 1 1 1  1 1 1 0  1 1 1 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x7EF0000
until_filterByAll               | 1 1 1  1 1 1 0  1 1 1 1  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x7EFE000
until_summary                   | 1 1 1  1 1 1 0  1 1 1 1  1 1 1 1  1 1 1 1  1 0 0 0  0 0 0 0 | 0x7EFFF80
whole_workflow                  | 1 1 1  1 1 1 0  1 1 1 1  1 1 1 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x7EFFFC0
from_phasing                    | 0 0 0  0 0 0 0  1 1 1 1  1 1 1 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x00FFFC0
from_phasing_to_summary         | 0 0 0  0 0 0 0  1 1 1 1  1 1 1 1  1 1 1 1  0 0 0 0  0 0 0 0 | 0x00FFF00
from_phasing_to_filterByAll     | 0 0 0  0 0 0 0  1 1 1 1  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x00FE000
from_phasing_to_qctools         | 0 0 0  0 0 0 0  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x00E0000
from_phasing_to_association     | 0 0 0  0 0 0 0  1 1 1 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x00F0000
from_phasing_to_qctools         | 0 0 0  0 0 0 0  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x00E0000
from_phasing_to_imputation      | 0 0 0  0 0 0 0  1 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0080000
from_imputation                 | 0 0 0  0 0 0 0  0 1 1 1  1 1 1 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x007FFC0
from_imputation_to_summary      | 0 0 0  0 0 0 0  0 1 1 1  1 1 1 1  1 1 1 1  1 0 0 0  0 0 0 0 | 0x007FF80
from_imputation_to_filterByAll  | 0 0 0  0 0 0 0  0 1 1 1  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x007E000
from_imputation_to_association  | 0 0 0  0 0 0 0  0 1 1 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0070000
from_imputation_to_filterByInfo | 0 0 0  0 0 0 0  0 1 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0040000
from_filterByInfo_to_qctoolS    | 0 0 0  0 0 0 0  0 0 1 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0020000
from_qctoolS_to_association     | 0 0 0  0 0 0 0  0 0 0 1  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x0010000
from_association                | 0 0 0  0 0 0 0  0 0 0 0  1 1 1 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x000FFC0
from_association_to_filterByAll | 0 0 0  0 0 0 0  0 0 0 0  1 1 1 0  0 0 0 0  0 0 0 0  0 0 0 0 | 0x000E000
from_association_to_summary     | 0 0 0  0 0 0 0  0 0 0 0  1 1 1 1  1 1 1 1  1 0 0 0  0 0 0 0 | 0x000FF80
from_filterByAll                | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  1 1 1 1  1 1 0 0  0 0 0 0 | 0x0001FC0
from_jointFiltered_to_condensed | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  1 0 0 0  0 0 0 0  0 0 0 0 | 0x0000800
from_filterByAll_to_summary     | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  1 1 1 1  1 0 0 0  0 0 0 0 | 0x0001F80
from_manhattan_to_combine       | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  0 0 1 0  0 0 0 0  0 0 0 0 | 0x0001200
from_combine_to_manhattan       | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  0 0 0 0  0 0 0 0 | 0x0000100
from_combine_to_summary         | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  1 0 0 0  0 0 0 0 | 0x0000180
from_combine                    | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 1  1 1 0 0  0 0 0 0 | 0x00001C0
from_combineGenManTop_to_summary| 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  1 0 0 0  0 0 0 0 | 0x0000080
from_summary                    | 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 0 0 0  0 1 0 0  0 0 0 0 | 0x0000040
-----------------------------------------------------------------------------------------------


convertFromBedToBed
createRsIdList
phasingBed
phasing
createListOfExcludedSnps
filterHaplotypes
imputeWithImpute
imputeWithMinimac
filterByInfo
qctoolS
snptest
collectSummary
mergeTwoChunks
filterByAll
jointCondensedFiles
jointFilteredByAllFiles
generateTopHits
generateQQManhattanPlots
combinePanelsComplex
combGenerateManhattanTop
phenoAnalysis
tasku
taskv
taskw
taskx
tasky
taskz
