bumped versions and docs

maxplanck-ie · Apr 10, 2024 · 94d9f36 · 94d9f36
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diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.8.1
+  version: 2.8.2
 
 source:
   path: ../

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,19 +1,21 @@
 snakePipes News
 ===============
 
-snakePipes x.y.z
+snakePipes 2.8.2
 ________________
 
 * added SEACR peaks qc
 * added external bed functionality for differential binding in ChIP-seq and ATAC-seq workflows
 * added "allelic-counting" mode to mRNA-seq, allowing to count reads and run DGE from allelic bam files split e.g. by whatshap
+* added support for custom model formula to mRNA-seq workflow
 * fixed copyfile command for sampleSheet
 * removed deprecated --force argument from mamba commands
 * fixes #998
 * fixes #997
 * fixes #996
-
-
+* fixes #994
+* fixes #1000
+* fixes #1001
 
 snakePipes 2.8.1
 ----------------

diff --git a/docs/content/workflows/mRNA-seq.rst b/docs/content/workflows/mRNA-seq.rst
@@ -144,6 +144,9 @@ Like the other workflows, differential expression can be performed using the ``-
 
 .. note:: The first entry defines which group of samples are control. This way, the order of comparison and likewise the sign of values can be changed. The DE analysis might fail if your sample names begin with a number. So watch out for that!
 
+
+Optionally, the user may submit their desired model formula (without the leading tilda ``~``)  with ``--formula``.
+
 Differential Splicing
 ---------------------
 

diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '2.8.1'
+__version__ = '2.8.2'
diff --git a/snakePipes/shared/defaults.yaml b/snakePipes/shared/defaults.yaml
@@ -7,7 +7,7 @@
 # permitted here.
 ################################################################################
 #
-condaEnvDir: '/package/mamba/envs/snakepipesenvs/2.8.1'
+condaEnvDir: '/package/mamba/envs/snakepipesenvs/2.8.2'
 snakemakeOptions: ''
 organismsDir: 'shared/organisms'
 clusterConfig: 'shared/cluster.yaml'
-Original file line number
+Diff line change
@@ Expand Up @@
     .. note:: The first entry defines which group of samples are control. This way, the order of comparison and likewise the sign of values can be changed. The DE analysis might fail if your sample names begin with a number. So watch out for that!
+    Optionally, the user may submit their desired model formula (without the leading tilda ``~``)  with ``--formula``.
     Differential Splicing
     ---------------------
@@ Expand Down @@