From 999e341046acc5ede5eddfbf632b2a6be7af719a Mon Sep 17 00:00:00 2001 From: Kai Zhang Date: Wed, 21 Apr 2021 18:40:14 -0700 Subject: [PATCH] update --- Taiji.cabal | 2 +- app/Main.hs | 5 +++-- src/Taiji/Core/RegulatoryElement.hs | 4 ++-- src/Taiji/SingleCell.hs | 2 +- stack.yaml | 35 ++++++++++++----------------- 5 files changed, 21 insertions(+), 27 deletions(-) diff --git a/Taiji.cabal b/Taiji.cabal index b7d78a5..fa7e89d 100644 --- 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 index f4ecbcd..e02599b 100644 --- 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 index 4ac5f20..8b6355b 100644 --- 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 index 6dab4d0..4547c30 100644 --- 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 index 165d754..88b8a09 100644 --- 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 \ No newline at end of file