fix: clean conda environments

workflow/envs/ashleys_base.yaml

@@ -3,19 +3,14 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - samtools
-  - tabix
+  - ashleys-qc
   - bwa
-  - sambamba
   - mosaicatcher
-  # - alfred
-  - ashleys-qc
+  - multiqc
   - pandas
-  # PUBLISHDIR
+  - python=3.9
   - rsync
-  # MULTIQC
-  - multiqc
-  # Fix sklearn update
-  - scikit-learn=1.2.2
-  # Fix ashleys GH issue
-  - python=3.10
+  - sambamba
+  - samtools
+  - scikit-learn=0.23.2
+  - tabix

workflow/envs/ashleys_rtools.yaml

@@ -2,49 +2,23 @@ name: rtools
 channels:
   - conda-forge
   - bioconda
-  - r
-  - anaconda
 dependencies:
-  # - bioconductor-biocparallel
-  # - bioconductor-bsgenome
-  # - bioconductor-bsgenome.hsapiens.ucsc.hg19
-  # - bioconductor-bsgenome.hsapiens.ucsc.hg38
-  # - bioconductor-fastseg
-  # - bioconductor-genomicalignments
+  - bioconductor-edger
   - bioconductor-genomicranges
-  # - bioconductor-rsamtools
-  # - bioconductor-s4vectors
+  - fonts-conda-forge
   - r-assertthat
   - r-base
-  # - r-biocmanager
+  - r-cairo
   - r-cowplot
   - r-data.table
-  # - r-devtools
-  # - r-doparallel
-  # - r-foreach
+  - r-dplyr
   - r-ggplot2
-  # - r-gtools
+  - r-ggpubr
+  - r-platetools
+  - r-r.utils
+  - r-rcolorbrewer
   - r-reshape2
-  # - r-zoo
-  # - r-dplyr
-  # - r-mc2d
-  # - r-pheatmap
-  # - bioconductor-complexheatmap
-  # - r-gplots
   - r-scales
-  - r-rcolorbrewer
-  # - r-stringr
-  - r-cairo
-  - fonts-anaconda
-  # NEW
-  - bioconductor-edger
-  - r-r.utils
-  # PLATE PLOT
-  - r-dplyr
-  - r-platetools
-  - r-viridis
-  # GC_correction
-  - r-tidyr
-  - r-ggpubr
-  # SOLVE R lib issue
   - r-stringi=1.7.12
+  - r-tidyr
+  - r-viridis