v1.1.0

Author: kaizhang

ChangeLog.md

@@ -7,6 +7,8 @@ Latest
 
 - Reduce memory usage in certain steps.
 
+- Fix the normalization issue in bigwig file generation.
+
 - Add more features to single cell RNA-seq analysis pipeline.
 
 - Add more features to single cell ATAC-seq analysis pipeline.
@@ -33,4 +35,4 @@ v0.5.0 (2018-10-28)
 ===================
 
 - Add a function to include external networks, using the field
-  `external_network` in the configuration file.
+  `external_network` in the configuration file.

LICENSE

@@ -1,4 +1,4 @@
-Copyright Author name here (c) 2017
+Copyright Kai Zhang (c) 2017-2020
 
 All rights reserved.
 

Taiji.cabal

@@ -1,5 +1,5 @@
 name:                Taiji
-version:             1.0.1.9
+version:             1.1.0
 synopsis:            Multi-omics bioinformatics analysis pipeline
 description:         Taiji is an integrated multi-omics bioinformatics analysis
                      pipeline. It can analyze ATAC-seq, RNA-seq, single cell
@@ -10,7 +10,7 @@ license:             BSD3
 license-file:        LICENSE
 author:              Kai Zhang
 maintainer:          [email protected]
-copyright:           (c) 2017-2019 Kai Zhang
+copyright:           (c) 2017-2020 Kai Zhang
 category:            Bio
 build-type:          Simple
 extra-source-files:
@@ -41,7 +41,7 @@ library
                      , bytestring
                      , bio-pipelines >= 0.1.2
                      , bio-experiments
-                     , bioinformatics-toolkit >= 0.9.0
+                     , bioinformatics-toolkit >= 0.9.1
                      , containers
                      , clustering
                      , double-conversion
@@ -58,7 +58,7 @@ library
                      , mtl
                      , singletons >= 2.5
                      , statistics >= 0.14.0
-                     , SciFlow >= 0.7.1
+                     , SciFlow >= 0.7.2
                      , temporary
                      , text
                      , vector

app/Main.hs

@@ -65,6 +65,7 @@ instance SCATACSeqConfig TaijiConfig where
     _scatacseq_cluster_resolution = _taiji_cluster_resolution
     _scatacseq_cluster_optimizer = _taiji_cluster_optimizer
     _scatacseq_doublet_score_cutoff = _taiji_scrna_doublet_score_cutoff 
+    _scatacseq_cluster_by_window = const False
 
 instance RNASeqConfig TaijiConfig where
     _rnaseq_assembly = _taiji_assembly

src/Taiji/Core.hs

@@ -54,13 +54,11 @@ builder = do
             return $ getHiCLoops hic
         |] $ doc .= "Read HiC loops from input file."
 
-    node "Create_Linkage_Prep" 'aggregate $
-        doc .= "Prepare for parallel execution."
+    node "Create_Linkage_Prep" 'aggregate $ return ()
     nodePar "Create_Linkage" 'saveAssociations $ memory .= 20
     path ["Create_Linkage_Prep", "Create_Linkage"]
 
-    node "Compute_Ranks_Prep" [| \(x, expr) -> return $ zip x $ repeat expr |] $
-        return ()
+    uNode "Compute_Ranks_Prep" [| \(x, expr) -> zip x $ repeat expr |]
     nodePar "Compute_Ranks" 'computeRanks $ do
         doc .= "Perform personalized Pagerank."
         memory .= 20

src/Taiji/SingleCell.hs

@@ -15,7 +15,7 @@ builder = do
     path ["Compute_Ranks_SC_Prep", "Compute_Ranks_SC"]
     -}
 
-    node "Compute_Ranks_SC_Prep" [| return . prepareData |] $ return ()
+    uNode "Compute_Ranks_SC_Prep" [| prepareData |]
     nodePar "Compute_Ranks_SC" 'computeRanksCluster $ return ()
     node "Output_Ranks_SC" [| outputRanksCluster "/Rank/Cluster/" |] $ return ()
     path ["Compute_Ranks_SC_Prep", "Compute_Ranks_SC", "Output_Ranks_SC"]

stack.yaml

@@ -9,30 +9,30 @@ extra-deps:
   commit:  f796c18ff3998713c2485d67f74c5e96367d285d
 
 - git:     https://github.com/Taiji-pipeline/bio-pipelines.git
-  commit:  50d65bc42b9331badc00bf387cecfbe008ad37e9
+  commit:  4b2feb52eb62dde1c26bb4a7e9c4d5456f6034b5
 
 - git:     https://github.com/Taiji-pipeline/bio-experiments.git
   commit:  470d1c09c8b8ecc64ced5f085c87cc66d70f8b9d
 
 - git:     https://github.com/Taiji-pipeline/Taiji-RNA-seq.git
-  commit:  0b184782b70c4200c4be829e92c3fed6d7de7572
+  commit:  384c714206e192e743e3c6de50a74f29fd62cf4e
 
 - git:     https://github.com/Taiji-pipeline/Taiji-ATAC-seq.git
-  commit:  e33ca8295342412ee4d32bfa4f0a7815db4221ce
+  commit:  fd5df5fa73946d4e4e836bb46d539248f983cd4d
 
 - git:     https://github.com/Taiji-pipeline/Taiji-scRNA-seq.git
-  commit:  6043a6572730ce02ee535119c35b22c5f227518a
+  commit:  b5d02b0aef22b11f60997f4e86ff67e512d4aa2f
 
 - git:     https://github.com/Taiji-pipeline/Taiji-scATAC-seq.git
-  commit:  0079329d422dec161dfbbfd6e44b94942bdbd077
+  commit:  75b79eb117251dc595712d41ef2f310f8301d5a1
 
 - git:     https://github.com/kaizhang/haskell-igraph.git
   commit:  e9db8aad4ca005257a464a5eff0e5ff15aa761b2
 
 - git:     https://github.com/kaizhang/HsHTSLib.git
   commit:  c116cfa29e33d3142a6cb502f1dc4c02066d0aa9
 
-- bioinformatics-toolkit-0.9.0
+- bioinformatics-toolkit-0.9.1
 
 - bbi-0.1.1
 - clustering-0.4.1
@@ -47,7 +47,7 @@ extra-deps:
 - distributed-process-monad-control-0.5.1.3
 
 - git:     https://github.com/kaizhang/SciFlow.git
-  commit:  ca5f37411e73c9066f67f7fe65f4a341946c7dfd
+  commit:  2b88b7f99f8c4555919a9746782984545d319006
   subdirs:
       - SciFlow
       - SciFlow-app