update

ChangeLog.md

@@ -1,9 +1,9 @@
 v1.3.0 (2021-07-18)
 ===================
 
-- First offical release of the single cell ATAC-seq pipeline.
-- A lof of improvments on single cell analysis pipeline.
-- Create signal enrichment bigwig file for the ATAC-seq pipeline.
+- First offcial release of the single-cell ATAC-seq pipeline.
+- A lot of improvments to single-cell analysis pipeline.
+- Create signal enrichment bigwig files for the ATAC-seq pipeline.
 - Bug fix: #19
 
 v1.2.1 (2020-06-27)

README.md

@@ -5,9 +5,23 @@ Taiji -- multi-omics bioinformatics pipeline
 ![Continuous integration](https://github.com/Taiji-pipeline/Taiji/workflows/Continuous%20integration/badge.svg)
 ![GitHub All Releases](https://img.shields.io/github/downloads/Taiji-pipeline/Taiji/total)
 
-Taiji is an integrated analysis pipeline for analyzing bulk/single-cell ATAC-seq and RNA-seq data.
+Taiji is an integrative analysis pipeline for analyzing bulk/single-cell ATAC-seq and RNA-seq data.
 Please go to this [website](https://taiji-pipeline.github.io/) for documentation and tutorials. 
 
+- Joint analysis of ATAC-seq, RNA-seq and Hi-C datasets.
+- Integrate multiple single cell datasets, scale to more than 1 million cells!
+
+The design philosophy of the Taiji pipeline is focused on:
+
+- Correctness: We only include reliable algorithms and
+    make every effort to ensure the implementations are bug-free.
+- Performance: We code algorithms from scratch when necessary to
+    ensure the pipeline can scale to large datasets (thousands of samples at least).
+- Convinence: Most analyses have multipe entry points, e.g., Fastq, Bam or Bed.
+    The execution of the pipeline requires only a single command.
+
+We achieve these at the expense of customization. This will be improved in the future.
+
 Installation
 ------------
 

Taiji.cabal

@@ -1,13 +1,13 @@
 name:                Taiji
-version:             1.3.0
+version:             1.3.1
 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
                      ATAC-seq, single cell RNA-seq datasets as well as
                      integrated analysis of different kinds of data.
 homepage:            https://taiji-pipeline.github.io/
 license:             BSD3
-license-file:        LICENSE
+license-file:         LICENSE
 author:              Kai Zhang
 maintainer:          [email protected]
 copyright:           (c) 2017-2021 Kai Zhang

app/Main.hs

@@ -29,7 +29,6 @@ import           Taiji.Pipeline.SC.ATACSeq.Types (SCATACSeqConfig (..))
 import           Taiji.Pipeline.RNASeq.Types (RNASeqConfig (..))
 import           Taiji.Pipeline.SC.RNASeq.Types (SCRNASeqConfig (..))
 
-
 instance ATACSeqConfig TaijiConfig where
     _atacseq_output_dir = (<> "/ATACSeq") . _taiji_output_dir
     _atacseq_input = _taiji_input
@@ -38,7 +37,7 @@ instance ATACSeqConfig TaijiConfig where
     _atacseq_genome_fasta = _taiji_genome
     _atacseq_genome_index = Just . _taiji_genome_index
     _atacseq_motif_file = _taiji_motif_file
-    _atacseq_bwa_seed_length = _taiji_bwa_seed_length
+    _atacseq_bwa_seed_length = fromMaybe 32 . _taiji_bwa_seed_length
     _atacseq_callpeak_opts config = def & mode .~ NoModel (-100) 200
         & cutoff .~ QValue (fromMaybe 0.05 $ _taiji_callpeak_fdr config)
         & callSummits .~ True

src/Taiji/Core.hs

@@ -49,7 +49,7 @@ builder = do
     node "HiC_Read_Input" [| \_ -> do
         input <- asks _taiji_input
         liftIO $ do
-            hic <- mkInputReader input "HiC" HiC
+            hic <- mkInputReader input "HiC" (\_ x -> HiC x)
             return $ getHiCLoops hic
         |] $ doc .= "Read HiC loops from input file."
 

stack.yaml

@@ -1,4 +1,4 @@
-resolver: lts-18.2
+resolver: lts-18.12
 
 packages:
 - '.'
@@ -12,31 +12,31 @@ flags:
 extra-deps:
 
 - git:     https://github.com/Taiji-pipeline/Taiji-utils.git
-  commit:  c970d24adcb3a4a141f7ee205ba2af60f7c65717
+  commit:  f5e009cf7a9a683f7e43bf97fb33c758ba13d97b
 
 - git:     https://github.com/Taiji-pipeline/bio-pipelines.git
-  commit:  251337aea1e9449c161b634fdb316f47f2f766f2
+  commit:  90f242992001be3672ddc2c1749beff432bbc5f3
 
 - git:     https://github.com/Taiji-pipeline/bio-experiments.git
-  commit:  48ff0a243df42796000b8caaf61f2907b92c7d95
+  commit:  12d62074c50f746482c3c2db4e5b47bc43803a60
 
 - git:     https://github.com/Taiji-pipeline/Taiji-RNA-seq.git
-  commit:  7f34241225f9033a96050bde6ba958b8519041af
+  commit:  a567e632e1167d7105974e1acf87be9f356fc494
 
 - git:     https://github.com/Taiji-pipeline/Taiji-ATAC-seq.git
-  commit:  9fc7181d071866279fbed19ffc5768d77ab5e66a
+  commit:  ba7a073b56bf4ca60a227d70b4508f2f83a57d16
 
 - git:     https://github.com/Taiji-pipeline/Taiji-scRNA-seq.git
-  commit:  f513e533dc23953fa65076bf2debc8c68c9f6d79
+  commit:  0362dc0fc0024ff474f4d582d048852444eac5b9
 
 - git:     https://github.com/Taiji-pipeline/Taiji-scATAC-seq.git
-  commit:  9e14e4ffb40b7834f10c0bb2cceaefca5ea6310f
+  commit:  6e912364ddce0f7ddcaae7938cd9696aac4937ca
 
 - git:     https://github.com/Taiji-pipeline/Taiji-fusion.git
   commit:  a2ef0b3c162028ba1bd89c7f151b3e703f4cde8d
 
 - git:     https://github.com/kaizhang/HsHTSLib.git
-  commit:  c116cfa29e33d3142a6cb502f1dc4c02066d0aa9
+  commit:  a2fcc435fc752152f06f14e0cfa56153fa0b7d02
 
 - git:     https://github.com/kaizhang/ChromVAR.git
   commit:  d64dd55579c8db9625028065b4cb3314e8f0c4a9
@@ -48,7 +48,7 @@ extra-deps:
   commit:  d790e030e6e08b04dc0971221b6054d6700d82e7
 
 - git:     https://github.com/kaizhang/bioinformatics-toolkit.git
-  commit:  89b8d1cdf4fa7b075794c37c070cab8ac27acfaf
+  commit:  463cb8d16230a0777072e8793338b89a7c420487
   subdirs:
       - bioinformatics-toolkit
 
@@ -63,7 +63,7 @@ extra-deps:
 - distributed-static-0.3.9
 
 - git:     https://github.com/kaizhang/SciFlow.git
-  commit:  c9d85008e9db598d2addc8fe999e1abad9147e1c
+  commit:  ee510340b54f4e2c416cc6e121c767885abce374
   subdirs:
       - SciFlow
       - SciFlow-app