From 65e7de219edd5766b7e4a155314343d587637067 Mon Sep 17 00:00:00 2001 From: Kai Zhang Date: Fri, 1 Oct 2021 11:13:28 -0700 Subject: [PATCH] update --- ChangeLog.md | 6 +++--- README.md | 16 +++++++++++++++- Taiji.cabal | 4 ++-- app/Main.hs | 3 +-- src/Taiji/Core.hs | 2 +- stack.yaml | 22 +++++++++++----------- 6 files changed, 33 insertions(+), 20 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index fe083a5..2615593 100644 --- a/ChangeLog.md +++ b/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) diff --git a/README.md b/README.md index e595992..a9577da 100644 --- a/README.md +++ b/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 ------------ diff --git a/Taiji.cabal b/Taiji.cabal index 86cb3ce..2ad13e7 100644 --- a/Taiji.cabal +++ b/Taiji.cabal @@ -1,5 +1,5 @@ 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 @@ -7,7 +7,7 @@ description: Taiji is an integrated multi-omics bioinformatics analysis 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: kai@kzhang.org copyright: (c) 2017-2021 Kai Zhang diff --git a/app/Main.hs b/app/Main.hs index 4022c8f..a2f2d57 100644 --- a/app/Main.hs +++ b/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 diff --git a/src/Taiji/Core.hs b/src/Taiji/Core.hs index 4be2f93..9146d5c 100644 --- a/src/Taiji/Core.hs +++ b/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." diff --git a/stack.yaml b/stack.yaml index 21fbfd7..b80326f 100644 --- a/stack.yaml +++ b/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