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

epigen · Dec 20, 2024 · 6613f9f · 6613f9f
1 parent ce16f56
commit 6613f9f
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Showing 8 changed files with 15 additions and 6 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/seurat_lda.yaml b/workflow/envs/seurat_lda.yaml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - r-seurat=4.4.0
   - r-irlba=2.3.5.1

diff --git a/workflow/envs/seurat_mixscape.yaml b/workflow/envs/seurat_mixscape.yaml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - r-seurat=4.4.0
   - r-matrix=1.6_5

diff --git a/workflow/rules/mixscape.smk b/workflow/rules/mixscape.smk
@@ -18,6 +18,8 @@ rule mixscape:
                                 "type": "Statistic",
                                 "misc": "PNG",
                                   }),
+    params:
+        utils_path = workflow.source_path("../scripts/utils.R"),
     resources:
         mem_mb=config.get("mem", "16000"),
     threads: 8*config.get("threads", 1)
@@ -47,6 +49,8 @@ rule lda:
                               "type": "UMAP",
                               "misc": "PNG",
                                   }),
+    params:
+        utils_path = workflow.source_path("../scripts/utils.R"),
     resources:
         mem_mb=config.get("mem", "16000"),
     threads: config.get("threads", 1)

diff --git a/workflow/rules/visualize.smk b/workflow/rules/visualize.smk
@@ -34,6 +34,8 @@ rule visualize:
                               "type": "Expression",
                               "misc": "Violin",
                                   }) if config["Antibody_Capture"]!="" else [],
+    params:
+        utils_path = workflow.source_path("../scripts/utils.R"),
     resources:
         mem_mb=config.get("mem", "16000"),
     threads: config.get("threads", 1)

diff --git a/workflow/scripts/lda.R b/workflow/scripts/lda.R
@@ -5,7 +5,8 @@ library("scales")
 
 # 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"]])
 
 # set expressions option to maximum to avoid "Error: protect(): protection stack overflow"
 # from here: https://stackoverflow.com/questions/32826906/how-to-solve-protection-stack-overflow-issue-in-r-studio

diff --git a/workflow/scripts/mixscape.R b/workflow/scripts/mixscape.R
@@ -4,7 +4,8 @@ library("ggplot2")
 
 # 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
 filtered_object_path <- snakemake@input[[1]]

diff --git a/workflow/scripts/visualize.R b/workflow/scripts/visualize.R
@@ -5,7 +5,8 @@ library("patchwork")
 
 # 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
 mixscape_object_path <- snakemake@input[["mixscape_object"]]