update

Taiji-pipeline · Apr 22, 2021 · 999e341 · 999e341
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Showing 5 changed files with 21 additions and 27 deletions.
diff --git a/Taiji.cabal b/Taiji.cabal
@@ -1,5 +1,5 @@
 name:                Taiji
-version:             1.2.2
+version:             1.2.2.2
 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

diff --git a/app/Main.hs b/app/Main.hs
@@ -67,10 +67,13 @@ instance SCATACSeqConfig TaijiConfig where
     _scatacseq_minimal_fragment = _scatac_minimal_fragment . _taiji_scatac_options
     _scatacseq_cluster_resolution_list = _scatac_cluster_resolution_list . _taiji_scatac_options
     _scatacseq_cluster_resolution = _scatac_cluster_resolution . _taiji_scatac_options
+    _scatacseq_do_subclustering = _scatac_do_subclustering . _taiji_scatac_options
     _scatacseq_subcluster_resolution = _scatac_subcluster_resolution . _taiji_scatac_options
     _scatacseq_cluster_optimizer = _scatac_cluster_optimizer . _taiji_scatac_options
+    _scatacseq_remove_doublets = _scatac_remove_doublets . _taiji_scatac_options
     _scatacseq_doublet_score_cutoff = _scatac_doublet_score_cutoff . _taiji_scatac_options
     _scatacseq_cluster_by_window = _scatac_cluster_by_window . _taiji_scatac_options
+    _scatacseq_cluster_exclude = _scatac_cluster_exclude . _taiji_scatac_options
     _scatacseq_window_size = _scatac_window_size . _taiji_scatac_options
     _scatacseq_cell_barcode_length = _scatac_cell_barcode_length . _taiji_scatac_options
 
@@ -113,8 +116,6 @@ build "wf" [t| SciFlow TaijiConfig |] $ do
 
     namespace "SCATAC" SCATACSeq.builder
     namespace "SCRNA" SCRNASeq.builder
-    --["SCATAC_Find_TFBS", "SCATAC_Make_CutSite_Index",
-    --    "DropSeq_Quantification" ] ~> "Compute_Ranks_SC_Prep"
     ["SCATAC_Find_TFBS", "SCATAC_Call_Peaks", "SCATAC_Gene_Acc"] ~>
         "Compute_Ranks_SC_Prep"
 

diff --git a/src/Taiji/Core/RegulatoryElement.hs b/src/Taiji/Core/RegulatoryElement.hs
@@ -92,8 +92,8 @@ mergeDomains regions = runIdentity $ runConduit $ mergeBedWith f regions .|
         sortBy (comparing (^._data)) xs
     mergeFn xs =
         let nm = head xs ^._data
-            beds = runIdentity $ runConduit $ mergeBed xs .| sinkList
-        in map (\x -> x & _data .~ nm) beds
+            beds = runIdentity $ runConduit $ mergeBed (map convert xs) .| sinkList
+        in map (\x -> BEDExt x nm) beds
 {-# INLINE mergeDomains #-}
 
 -- | Compute the 2D distal domains (enhancer regions) for a list of genes.

diff --git a/src/Taiji/SingleCell.hs b/src/Taiji/SingleCell.hs
@@ -38,7 +38,7 @@ computeRanksCluster (tfFl, ((nm, peakFl), expr)) = do
     liftIO $ do
         expr' <- (fmap . fmap) (\(a,b) -> (logBase 2 $ a + 1, exp b)) $
             readExpression 1 nm $ expr^.location
-        openRegions <- readBed $ peakFl ^.location
+        openRegions <- runResourceT $ runConduit $ streamBedGzip (peakFl ^.location) .| sinkList
         idx <- openBBs tfFl
         ranks <- getRanks (findActivePromoters openRegions promoters)
             expr' openRegions idx

diff --git a/stack.yaml b/stack.yaml
@@ -11,12 +11,11 @@ flags:
 
 extra-deps:
 
-#- git:     https://github.com/Taiji-pipeline/Taiji-utils.git
-#  commit:  3e8ffe4db15cc05b838c9931bac1661bf1eb700a
-- '../Taiji-utils'
+- git:     https://github.com/Taiji-pipeline/Taiji-utils.git
+  commit:  d28830609a4719e0310636971ac7ddd17a02504a 
 
 - git:     https://github.com/Taiji-pipeline/bio-pipelines.git
-  commit:  a001951bd3a91f1b35870f929019d838dc941778
+  commit:  6a7a615a23d7f17287698fe205347924b470b7f5
 
 - git:     https://github.com/Taiji-pipeline/bio-experiments.git
   commit:  40543900821258e4186d8fc1c0a0538d50c41d59
@@ -27,13 +26,11 @@ extra-deps:
 - git:     https://github.com/Taiji-pipeline/Taiji-ATAC-seq.git
   commit:  1b851f71b41ace8a731fe3188f9eeed457a034e2
 
-#- git:     https://github.com/Taiji-pipeline/Taiji-scRNA-seq.git
-#  commit:  8a3c6f6ebb60aee244e581d78390389e346b60c5
-- '../Taiji-scRNA-seq'
+- git:     https://github.com/Taiji-pipeline/Taiji-scRNA-seq.git
+  commit:  f513e533dc23953fa65076bf2debc8c68c9f6d79
 
-#- git:     https://github.com/Taiji-pipeline/Taiji-scATAC-seq.git
-#  commit:  4cbedcfa1425124a8eb322f9668ed34e04fdf963
-- '../Taiji-scATAC-seq'
+- git:     https://github.com/Taiji-pipeline/Taiji-scATAC-seq.git
+  commit:  cf8c110783c09700220b7e5e4368501ab2c3b0f7
 
 - git:     https://github.com/Taiji-pipeline/Taiji-fusion.git
   commit:  a2ef0b3c162028ba1bd89c7f151b3e703f4cde8d
@@ -51,7 +48,7 @@ extra-deps:
   commit:  d790e030e6e08b04dc0971221b6054d6700d82e7
 
 - git:     https://github.com/kaizhang/bioinformatics-toolkit.git
-  commit:  426ee4e6ddb620579d4483fb692ed454077b807b
+  commit:  89b8d1cdf4fa7b075794c37c070cab8ac27acfaf
   subdirs:
       - bioinformatics-toolkit
 
@@ -65,13 +62,9 @@ extra-deps:
 - network-transport-tcp-0.8.0
 - distributed-static-0.3.9
 
-#- git:     https://github.com/kaizhang/SciFlow.git
-#  commit:  c094c0483afa1e262c6048101d2566a76e2e9b19
-#  subdirs:
-#      - SciFlow
-#      - SciFlow-app
-#      - SciFlow-remote
-
-- '../../SciFlow/SciFlow'
-- '../../SciFlow/SciFlow-app'
-- '../../SciFlow/SciFlow-remote'
+- git:     https://github.com/kaizhang/SciFlow.git
+  commit:  c9d85008e9db598d2addc8fe999e1abad9147e1c
+  subdirs:
+      - SciFlow
+      - SciFlow-app
+      - SciFlow-remote