Merge branch 'master' into dev

gagneurlab · May 28, 2024 · abf9d0f · abf9d0f
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diff --git a/README.md b/README.md
@@ -3,6 +3,7 @@
 [![Version](https://img.shields.io/github/v/release/gagneurlab/drop?include_prereleases)](https://github.com/gagneurlab/drop/releases)
 [![Version](https://readthedocs.org/projects/gagneurlab-drop/badge/?version=latest)](https://gagneurlab-drop.readthedocs.io/en/latest)
 
+
 The detection of RNA Outliers Pipeline (DROP) is an integrative workflow to detect aberrant expression, aberrant splicing, and mono-allelic expression from raw RNA sequencing data. 
 
 The manuscript is available in [Nature Protocols](https://www.nature.com/articles/s41596-020-00462-5).
@@ -11,6 +12,7 @@ This [website](https://cmm.in.tum.de/public/paper/drop_analysis/webDir/drop_anal
 
 This [video](https://www.youtube.com/watch?v=XvgjiFQClhM&t=2761s) presents the tools used in DROP and their application to rare disease diagnostics.
 
+
 <img src="drop_sticker.png" alt="drop logo" width="200" class="center"/>
 
 
@@ -21,9 +23,11 @@ We recommend using a dedicated conda environment (`drop_env` in this example). I
 mamba create -n drop_env -c conda-forge -c bioconda drop --override-channels
 ```
 
+
 In the case troubles with mamba or conda, we recommend using the fixed `DROP_<version>.yaml` installation file we make available on our [public server](https://www.cmm.in.tum.de/public/paper/drop_analysis/). Install the current version and use the full path in the following command to install the conda environment `drop_env`
 ```
 mamba env create -f DROP_1.4.0.yaml
+
 ```
 
 Test installation with demo project
@@ -47,7 +51,9 @@ For more information on different installation options, refer to the
 
 ## What's new
 
+
 Version 1.4.0 fixes some bugs regarding the split reads counting for FRASER, which only affects cohorts containing samples with different strands (stranded forward, stranded reverse or unstranded). If your cohort contained samples with different strands, please rerun the AS module using version 1.4.0. In addition, due to snakemake updates affecting wBuild and the way we installed FRASER, installing DROP 1.3.3 no longer works. Version 1.3.4 fixes the FRASER version to ensure reproducibility and fixes certain scripts affected by the snakemake update. Running the pipeline with version 1.3.4 should provide the same outlier results as 1.3.3.
+Due to snakemake updates affecting wBuild and the way we installed FRASER, installing DROP 1.3.3 no longer works. Version 1.3.4 simply fixes the FRASER version to ensure reproducibility and fixes certain scripts affected by the snakemake update. Running the pipeline with the version 1.3.4 should provide the same outlier results as 1.3.3.
 
 Version 1.3.0 introduces the option to use FRASER 2.0 which is an improved version of FRASER that uses the Intron Jaccard Index metric instead of percent spliced in and splicing efficiency to quantify and later call aberrant splicing. To run FRASER 2.0, modify the `FRASER_version` parameter in the aberrantSplicing dictionary in the config file and adapt the `quantileForFiltering` and `deltaPsiCutoff` parameters. See the [config template](https://github.com/gagneurlab/drop/blob/master/drop/template/config.yaml) for more details. When switching between FRASER versions, we recommend running DROP in a
 separate folder for each version. Moreover, DROP now allows users to provide lists of genes to focus on and do the multiple testing correction instead of the usual transcriptome-wide approach. Refer to the [documentation](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html#limiting-fdr-correction-to-subsets-of-genes-of-interest).
@@ -56,9 +62,11 @@ separate folder for each version. Moreover, DROP now allows users to provide lis
 
 As of version 1.2.1 DROP has a new module that performs RNA-seq variant calling. The input are BAM files and the output either a single-sample or a multi-sample VCF file (option specified by the user) annotated with allele frequencies from gnomAD (if specified by the user). The sample annotation table does not need to be changed, but several new parameters in the config file have to be added and tuned. For more info, refer to the [documentation](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html#rna-variant-calling-dictionary).
 
+
 Also, as of version 1.2.1 the integration of external split and non-split counts to detect aberrant splicing is now possible. In a new column in the sample annotation, simply specify the directory containing the counts. For more info, refer to the [documentation](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html#external-count-examples).
 
 
+
 ## Set up a custom project
 Install the drop module according to [installation](#installation) and initialize the project in a custom project directory.
 ### Prepare the input data

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -27,6 +27,7 @@
 
 
 
+
 # -- General configuration ---------------------------------------------------
 
 master_doc = 'index'

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -22,6 +22,7 @@ Install the latest version and use the full path in the following command to ins
 
     mamba env create -f DROP_1.4.0.yaml
 
+
 Installation time: ~ 10min
 
 We can test whether the pipeline runs through by setting up the demo dataset in an empty directory (e.g. ``~/drop_demo``).

diff --git a/drop/__init__.py b/drop/__init__.py
@@ -4,5 +4,5 @@
 from . import utils
 from . import demo
 
-__version__ = "1.4.0"
 
+__version__ = "1.4.0"
diff --git a/drop/cli.py b/drop/cli.py
@@ -17,6 +17,7 @@
 
 @click.group()
 @click_log.simple_verbosity_option(logger)
+
 @click.version_option('1.4.0',prog_name='drop')
 
 

diff --git a/drop/installRPackages.R b/drop/installRPackages.R
@@ -23,18 +23,20 @@ if (file.exists(args[1])){
         package=gsub("=.*", "", unlist(args)),
         version=gsub(".*=", "", unlist(args)),
         ref="")
-    packages[package == version, version:=NA]
+    packages[package == version, c("min_version", "max_version") := ""]
 }
 installed <- as.data.table(installed.packages())
 
 for (pckg_name in packages$package) {
     package_dt <- packages[package == pckg_name]
     pckg_name <- gsub(".*/", "", pckg_name)
-    version <- package_dt$version
+    min_version <- package_dt$min_version
+    max_version <- package_dt$max_version
     branch <- package_dt$ref
 
-    if (!pckg_name %in% installed$Package || (!is.na(version) && compareVersion(
-        installed[Package == pckg_name, Version], version) < 0)) {
+    if (!pckg_name %in% installed$Package || (min_version != "" && (compareVersion(
+      installed[Package == pckg_name, Version], min_version) < 0 || compareVersion(
+        installed[Package == pckg_name, Version], max_version) > 0))) {
 
         package <- package_dt$package
         message(paste("install", package))

diff --git a/drop/requirementsR.txt b/drop/requirementsR.txt
@@ -1,4 +1,4 @@
-package	version	ref
+package	min_version	max_version	ref
 devtools
 gagneurlab/OUTRIDER	1.20.1	1.20.1
 gagneurlab/FRASER	1.99.4	1.99.4

diff --git a/setup.cfg b/setup.cfg
@@ -1,4 +1,5 @@
 [bumpversion]
+
 current_version = 1.4.0
 commit = True
 

diff --git a/setup.py b/setup.py
@@ -23,6 +23,7 @@
     name="drop",
     version="1.4.0",
 
+
     author="Vicente A. Yépez, Michaela Müller, Nicholas H. Smith, Daniela Klaproth-Andrade, Luise Schuller, Ines Scheller, Christian Mertes <mertes@in.tum.de>, Julien Gagneur <gagneur@in.tum.de>",
     author_email="yepez@in.tum.de",
     description="Detection of RNA Outlier Pipeline",