comment global.yaml and add nodefaults

epigen · Dec 20, 2024 · fbe83ca · fbe83ca
1 parent ede22fe
commit fbe83ca
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Showing 8 changed files with 8 additions and 8 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -1,6 +1,6 @@
 
 ##### global workflow dependencies #####
-conda: "envs/global.yaml"
+# conda: "envs/global.yaml"
 
 # libraries
 import yaml

diff --git a/workflow/envs/ComplexHeatmap.yaml b/workflow/envs/ComplexHeatmap.yaml
@@ -2,7 +2,7 @@ channels:
   - conda-forge
   - bioconda
   - r
-  - defaults
+  - nodefaults
 dependencies:
   - bioconductor-complexheatmap=2.10.0
   - r-rcolorbrewer=1.1_3

diff --git a/workflow/envs/cqn.yaml b/workflow/envs/cqn.yaml
@@ -2,7 +2,7 @@ name: cqn
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - bioconductor-cqn=1.44.0
   - r-data.table=1.15.2
diff --git a/workflow/envs/edgeR.yaml b/workflow/envs/edgeR.yaml
@@ -2,7 +2,7 @@ name: edgeR
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - bioconductor-edger=3.32.1
   - bioconductor-limma=3.46.0

diff --git a/workflow/envs/ggplot.yaml b/workflow/envs/ggplot.yaml
@@ -2,7 +2,7 @@ name: ggplot
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - r-ggplot2=3.4.2
   - r-patchwork=1.1.2

diff --git a/workflow/envs/python_basics.yaml b/workflow/envs/python_basics.yaml
@@ -2,7 +2,7 @@ name: python_basics
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - python=3.10
   - pandas=1.5.3

diff --git a/workflow/envs/reComBat.yaml b/workflow/envs/reComBat.yaml
@@ -2,7 +2,7 @@ name: reComBat
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - python=3.10
   - scikit-learn=1.3.0

diff --git a/workflow/scripts/plot_diagnostics.R b/workflow/scripts/plot_diagnostics.R
@@ -221,7 +221,7 @@ cfa_plot <- ggplot(log_p_values_melted, aes(x = PC, y = Metadata, fill = value))
                             ) 
 
 # determine plot size
-heigth_hm <- dim(p_values)[1] * 0.2
+heigth_hm <- dim(p_values)[1] * 0.2 + 1
 width_hm <- dim(p_values)[2] * 0.75 + 1
 
 # save plot