diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index d7538294e..f9aabba44 100755 --- 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 index 5adf8224b..fcbefb31e 100644 --- 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 index a0e6a5cf0..4393ea282 100644 --- 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 index 80e22f7ae..964a32ab4 100755 --- 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 index 1975203cb..f35badc8a 100755 --- 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'