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

workflow/Snakefile

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

workflow/envs/inspectdf.yaml

@@ -1,6 +1,6 @@
 channels:
   - conda-forge
-  - defaults
+  - nodefaults
 dependencies:
   - r-inspectdf=0.0.12
   - r-data.table=1.14.10

workflow/envs/seurat.yaml

@@ -1,7 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
   - r-seurat=4.4.0
   - bioconductor-glmgampoi=1.14.0

workflow/rules/normalize_correct_score.smk

@@ -29,6 +29,7 @@ rule normalize:
         confounders = [],
         module_gene_lists = config["module_gene_lists"],
         cell_cycle = config["cell_cycle"],
+        utils_path = workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/sctransform_cellScore.R"
 
@@ -65,5 +66,6 @@ rule correct:
         confounders = config["variables_to_regress"],
         module_gene_lists = config["module_gene_lists"],
         cell_cycle = config["cell_cycle"],
+        utils_path = workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/sctransform_cellScore.R"

workflow/rules/process.smk

@@ -1,3 +1,4 @@
+
 # load & generate Seurat object per sample including metadata
 rule prepare:
     input:
@@ -24,6 +25,7 @@ rule prepare:
         os.path.join("logs","rules","PREP_{sample}.log"),
     params:
         metadata = lambda w: "" if pd.isna(annot.loc["{}".format(w.sample),'metadata']) else annot.loc["{}".format(w.sample),'metadata'],
+        utils_path = workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/prepare.R"
 
@@ -53,7 +55,8 @@ rule merge:
     log:
         os.path.join("logs","rules","merge.log"),
     params:
-        extra_metadata = config["extra_metadata"]
+        extra_metadata = config["extra_metadata"],
+        utils_path = workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/merge.R"
 
@@ -74,6 +77,8 @@ rule split:
                               "list": "Metadata",
                               "feature": "",
                                 }),
+    params:
+        utils_path = workflow.source_path("../scripts/utils.R"),
     resources:
         mem_mb=config.get("mem", "16000"),
     threads: config.get("threads", 1)
@@ -114,6 +119,7 @@ rule filter_cells:
         ab_flag = config["modality_flags"]['Antibody_Capture'],
         crispr_flag = config["modality_flags"]['CRISPR_Guide_Capture'],
         custom_flag = config["modality_flags"]['Custom'],
+        utils_path = workflow.source_path("../scripts/utils.R"),
     script:
         "../scripts/filter.R"
 
@@ -145,6 +151,8 @@ rule pseudobulk:
                               "list": "Cell count",
                               "feature": "",
                                 }),
+    params:
+        utils_path = workflow.source_path("../scripts/utils.R"),
     resources:
         mem_mb=config.get("mem", "16000"),
     threads: config.get("threads", 1)

workflow/rules/visualize.smk

@@ -1,3 +1,4 @@
+
 # visualize metadata
 rule metadata_plots:
     input:
@@ -16,6 +17,8 @@ rule metadata_plots:
                                 "feature": "",
                                 }),
         metadata_stats = directory(os.path.join(result_path,'{split}','{step}','stats')),
+    params:
+        utils_path = workflow.source_path("../scripts/utils.R"),
     resources:
         mem_mb=config.get("mem", "16000"),
     threads: config.get("threads", 1)
@@ -44,6 +47,8 @@ rule seurat_plots:
                 "list": "{feature_list}",
                 "feature": "{feature}",
             }),
+    params:
+        utils_path = workflow.source_path("../scripts/utils.R"),
     resources:
         mem_mb=config.get("mem", "16000"),
     threads: config.get("threads", 1)

workflow/scripts/filter.R

@@ -5,7 +5,8 @@ library("Seurat")
 
 # 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
 raw_object_path <- snakemake@input[["raw_object"]]

workflow/scripts/merge.R

@@ -3,7 +3,8 @@ library("Seurat")
 
 # 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"]])
 
 #### configs
 

workflow/scripts/metadata_plot.R

@@ -6,7 +6,8 @@ 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
 metadata_path <- snakemake@input[["metadata"]]

workflow/scripts/prepare.R

@@ -4,7 +4,8 @@ library("Seurat")
 
 # 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"]])
 
 # helper function to assign each cell's gRNA and KO calls
 assign_grna_KO <- function(col) {

workflow/scripts/pseudobulk.R

@@ -7,7 +7,8 @@ library("dplyr")
 
 # 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"]])
 
 # helper function to check if all values in a group are the same
 all_equal <- function(x) {

workflow/scripts/sctransform_cellScore.R

@@ -5,7 +5,8 @@ library("sctransform")
 
 # 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[["filtered_object"]]

workflow/scripts/seurat_plots.R

@@ -5,7 +5,8 @@ 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
 object_path <- snakemake@input[["norm_object"]]

workflow/scripts/split.R

@@ -4,7 +4,8 @@ library("Seurat")
 
 # 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
 merged_object_path <- snakemake@input[["merged_object"]]