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

epigen · Dec 20, 2024 · eb2f051 · eb2f051
1 parent 0f844f5
commit eb2f051
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Showing 10 changed files with 14 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 os

diff --git a/workflow/envs/ggplot.yaml b/workflow/envs/ggplot.yaml
@@ -1,6 +1,6 @@
 channels:
   - conda-forge
-  - defaults
+  - nodefaults
 dependencies:
   - r-ggplot2=3.4.2
   - r-data.table=1.14.8
diff --git a/workflow/envs/heatmap.yaml b/workflow/envs/heatmap.yaml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - r-ggplot2=3.4.2
   - r-ggplotify=0.1.0

diff --git a/workflow/envs/seurat.yaml b/workflow/envs/seurat.yaml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - r-seurat=4.4.0
   - bioconductor-limma=3.58.1

diff --git a/workflow/envs/volcanos.yaml b/workflow/envs/volcanos.yaml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - bioconductor-enhancedvolcano=1.20.0
   - r-data.table=1.14.10

diff --git a/workflow/rules/dea.smk b/workflow/rules/dea.smk
@@ -55,6 +55,7 @@ rule aggregate:
         assay = lambda w: annot_dict["{}".format(w.analysis)]["assay"],
         metadata = lambda w: annot_dict["{}".format(w.analysis)]["metadata"],
         control = lambda w: annot_dict["{}".format(w.analysis)]["control"],
+        utils_path = workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/aggregate.R"
 
@@ -80,5 +81,6 @@ rule feature_lists:
         assay = lambda w: annot_dict["{}".format(w.analysis)]["assay"],
         metadata = lambda w: annot_dict["{}".format(w.analysis)]["metadata"],
         control = lambda w: annot_dict["{}".format(w.analysis)]["control"],
+        utils_path = workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/aggregate.R"
diff --git a/workflow/rules/visualize.smk b/workflow/rules/visualize.smk
@@ -25,6 +25,7 @@ rule volcanos:
         assay = lambda w: annot_dict["{}".format(w.analysis)]["assay"],
         metadata = lambda w: annot_dict["{}".format(w.analysis)]["metadata"],
         control = lambda w: annot_dict["{}".format(w.analysis)]["control"],
+        utils_path = workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/volcanos.R"
 

diff --git a/workflow/scripts/aggregate.R b/workflow/scripts/aggregate.R
@@ -2,7 +2,8 @@
 
 # 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"]]

diff --git a/workflow/scripts/heatmap.R b/workflow/scripts/heatmap.R
@@ -5,7 +5,8 @@ library("reshape2")
 
 # 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[["results"]]

diff --git a/workflow/scripts/volcanos.R b/workflow/scripts/volcanos.R
@@ -6,7 +6,8 @@ options(ragg.max_dim = 100000) # required for large volcano panels
 
 # 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[["results"]]