From 6722d287d4797933584fa1dba5dfed6074223f51 Mon Sep 17 00:00:00 2001
From: Kai Zhang <kai@kzhang.org>
Date: Sun, 18 Jul 2021 07:17:42 -0700
Subject: [PATCH] v1.3.0

---
 ChangeLog.md |  3 ++-
 Taiji.cabal  |  2 +-
 app/Main.hs  |  2 +-
 stack.yaml   | 18 +++++++++---------
 4 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/ChangeLog.md b/ChangeLog.md
index 52ebbeb..fe083a5 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -1,6 +1,7 @@
-v1.2.2 ()
+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.
 - Bug fix: #19
diff --git a/Taiji.cabal b/Taiji.cabal
index fa7e89d..86cb3ce 100644
--- a/Taiji.cabal
+++ b/Taiji.cabal
@@ -1,5 +1,5 @@
 name:                Taiji
-version:             1.2.2.2
+version:             1.3.0
 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
diff --git a/app/Main.hs b/app/Main.hs
index e02599b..4022c8f 100644
--- a/app/Main.hs
+++ b/app/Main.hs
@@ -29,6 +29,7 @@ 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
@@ -70,7 +71,6 @@ instance SCATACSeqConfig TaijiConfig where
     _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
diff --git a/stack.yaml b/stack.yaml
index 88b8a09..21fbfd7 100644
--- a/stack.yaml
+++ b/stack.yaml
@@ -1,4 +1,4 @@
-resolver: lts-17.4
+resolver: lts-18.2
 
 packages:
 - '.'
@@ -12,25 +12,25 @@ flags:
 extra-deps:
 
 - git:     https://github.com/Taiji-pipeline/Taiji-utils.git
-  commit:  d28830609a4719e0310636971ac7ddd17a02504a 
+  commit:  c970d24adcb3a4a141f7ee205ba2af60f7c65717
 
 - git:     https://github.com/Taiji-pipeline/bio-pipelines.git
-  commit:  6a7a615a23d7f17287698fe205347924b470b7f5
+  commit:  251337aea1e9449c161b634fdb316f47f2f766f2
 
 - git:     https://github.com/Taiji-pipeline/bio-experiments.git
-  commit:  40543900821258e4186d8fc1c0a0538d50c41d59
+  commit:  48ff0a243df42796000b8caaf61f2907b92c7d95
 
 - git:     https://github.com/Taiji-pipeline/Taiji-RNA-seq.git
   commit:  7f34241225f9033a96050bde6ba958b8519041af
 
 - git:     https://github.com/Taiji-pipeline/Taiji-ATAC-seq.git
-  commit:  1b851f71b41ace8a731fe3188f9eeed457a034e2
+  commit:  9fc7181d071866279fbed19ffc5768d77ab5e66a
 
 - git:     https://github.com/Taiji-pipeline/Taiji-scRNA-seq.git
   commit:  f513e533dc23953fa65076bf2debc8c68c9f6d79
 
 - git:     https://github.com/Taiji-pipeline/Taiji-scATAC-seq.git
-  commit:  cf8c110783c09700220b7e5e4368501ab2c3b0f7
+  commit:  9e14e4ffb40b7834f10c0bb2cceaefca5ea6310f
 
 - git:     https://github.com/Taiji-pipeline/Taiji-fusion.git
   commit:  a2ef0b3c162028ba1bd89c7f151b3e703f4cde8d
@@ -56,8 +56,8 @@ extra-deps:
 - clustering-0.4.1
 - jmacro-0.6.17
 
-- git:     https://github.com/patrickt/distributed-process.git
-  commit:  645bc55c1b0b0d18227d1fc093379967c74af669
+- git:     https://github.com/Taiji-pipeline/distributed-process.git
+  commit:  e143f6bce9d7f1e13b0d12f11763f6f24d2da4df
 - distributed-process-monad-control-0.5.1.3
 - network-transport-tcp-0.8.0
 - distributed-static-0.3.9
@@ -67,4 +67,4 @@ extra-deps:
   subdirs:
       - SciFlow
       - SciFlow-app
-      - SciFlow-remote
\ No newline at end of file
+      - SciFlow-remote