fix: env update (#42)

* fix: updated to current snakemake and python

* fix: preliminary env update

* fix: removed unnecessary bioconductor and r dependencies

* fix: added biopython dependency

---------

Co-authored-by: Yannic Eising <yeising@students.uni-mainz.de>

workflow/envs/env.yml

@@ -3,30 +3,24 @@ channels:
     - r
     - bioconda
 dependencies:
-    - python>=3.12.1
-    - snakemake>=8.4.8
+    - python>=3.12.4
+    - snakemake>=8.14.0
     - snakemake-executor-plugin-slurm
     - snakemake-storage-plugin-fs
     - snakemake-interface-common
     - snakemake-interface-storage-plugins
-    - bioconductor-genomicfeatures
-    - bioconductor-drimseq
-    - bioconductor-edger
-    - bioconductor-dexseq
-    - bioconductor-stager
-    - minimap2
+    - minimap2=2.28
     - samtools
-    - r-dplyr
-    - r-tidyr
     - pysam
     - pandas
-    - salmon=1.9.0
+    - salmon=1.10.3
     - nanoplot
     - matplotlib
     - seaborn
     - pydeseq2=0.4.4
     - anndata>=0.8.0
-    - ensureconda
+    - ensureconda=1.4.4
     - gffread>=0.12.7
     - qualimap>=2.3
     - snakemake-wrapper-utils>=0.6.2
+    - biopython >=1.84