comment global.yaml, add nodefaults and replace snakemake@source

Author: sreichl

workflow/Snakefile

@@ -1,6 +1,6 @@
 
 ##### global workflow dependencies #####
-conda: "envs/global.yaml"
+# conda: "envs/global.yaml"
 
 ##### libraries #####
 import os

workflow/envs/ggplot.yaml

@@ -1,6 +1,6 @@
 channels:
   - conda-forge
-  - defaults
+  - nodefaults
 dependencies:
   - r-ggplot2=3.3.6
   - r-data.table=1.15.2

workflow/envs/heatmap.yaml

@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - r-ggplot2=3.5.1
   - r-ggplotify=0.1.2

workflow/envs/limma.yaml

@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - bioconductor-limma=3.46.0
   - bioconductor-edger=3.32.1

workflow/envs/volcanos.yaml

@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - bioconductor-enhancedvolcano=1.20.0
   - r-ggplot2=3.5.1

workflow/rules/dea.smk

@@ -75,6 +75,7 @@ rule aggregate:
         adj_pval = config["filters"]["adj_pval"],
         lfc = config["filters"]["lfc"],
         ave_expr = config["filters"]["ave_expr"],
+        utils_path=workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/aggregate.R"
 
@@ -104,5 +105,6 @@ rule feature_lists:
         adj_pval = config["filters"]["adj_pval"],
         lfc = config["filters"]["lfc"],
         ave_expr = config["filters"]["ave_expr"],
+        utils_path=workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/aggregate.R"

workflow/rules/visualize.smk

@@ -24,6 +24,7 @@ rule volcanos:
     params:
         pCutoff = config["volcano"]["pCutoff"],
         FCcutoff = config["volcano"]["FCcutoff"],
+        utils_path=workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/volcanos.R"
 
@@ -52,5 +53,6 @@ rule lfc_heatmap:
         adj_pval = config["filters"]["adj_pval"],
         lfc = config["filters"]["lfc"],
         ave_expr = config["filters"]["ave_expr"],
+        utils_path=workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/heatmap.R"

workflow/scripts/aggregate.R

@@ -4,7 +4,8 @@ library("data.table")
 
 # source utility functions
 # source("workflow/scripts/utils.R")
-snakemake@source("./utils.R")
+# snakemake@source("./utils.R") # does not work when loaded as module (https://github.com/snakemake/snakemake/issues/2205)
+source(snakemake@params[["utils_path"]])
 
 # inputs
 dea_result_path <- snakemake@input[["dea_results"]]

workflow/scripts/heatmap.R

@@ -8,7 +8,8 @@ library("data.table")
 
 # source utility functions
 # source("workflow/scripts/utils.R")
-snakemake@source("./utils.R")
+# snakemake@source("./utils.R") # does not work when loaded as module (https://github.com/snakemake/snakemake/issues/2205)
+source(snakemake@params[["utils_path"]])
 
 # inputs
 # dea_lfc_path <- snakemake@input[["dea_lfc"]]

workflow/scripts/volcanos.R

@@ -6,7 +6,8 @@ library("data.table")
 
 # source utility functions
 # source("workflow/scripts/utils.R")
-snakemake@source("utils.R")
+# snakemake@source("./utils.R") # does not work when loaded as module (https://github.com/snakemake/snakemake/issues/2205)
+source(snakemake@params[["utils_path"]])
 
 # inputs
 dea_result_path <- snakemake@input[["dea_results"]]