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