adapt to Snakemake 8; move env, config, annot export into the result …

…folder to be self-contained

README.md

@@ -1,7 +1,7 @@
 [![DOI](https://zenodo.org/badge/481635018.svg)](https://zenodo.org/badge/latestdoi/481635018)
 
 # scCRISPR-seq Perturbation Analysis Snakemake Workflow using Seurat's Mixscape
-A [Snakemake](https://snakemake.readthedocs.io/en/stable/) workflow for performing perturbation analyses of pooled (multimodal) CRISPR screens with scRNA-seq read-out (scCRISPR-seq, CROP-seq, Perturb-seq) powered by the R package [Seurat's](https://satijalab.org/seurat/index.html) method [Mixscape](https://satijalab.org/seurat/articles/mixscape_vignette.html).
+A [Snakemake 8](https://snakemake.readthedocs.io/en/stable/) workflow for performing perturbation analyses of pooled (multimodal) CRISPR screens with scRNA-seq read-out (scCRISPR-seq, CROP-seq, Perturb-seq) powered by the R package [Seurat's](https://satijalab.org/seurat/index.html) method [Mixscape](https://satijalab.org/seurat/articles/mixscape_vignette.html).
 
 This workflow adheres to the module specifications of [MR.PARETO](https://github.com/epigen/mr.pareto), an effort to augment research by modularizing (biomedical) data science. For more details, instructions and modules check out the project's repository. Please consider starring and sharing modules that are useful to you, this helps me in prioritizing my efforts!
 

config/README.md

@@ -1,8 +1,10 @@
 # Configuration
 
-You need one configuration file and one annotation file to run the complete workflow. You can use the provided example as starting point. If in doubt read the comments in the config and/or try the default values.
+You need one configuration file and one annotation file to run the complete workflow. If in doubt read the comments in the config and/or try the default values.
 
-- project configuration (config/config.yaml): different for every project/dataset and configures the analyses to be performed.
+- project configuration (`config/config.yaml`): different for every project/dataset and configures the analyses to be performed.
 - sample annotation (sample_annotation): CSV file consisting of two columns
     -  name: name of the dataset (tip: keep it short).
     -  data: absolute path to the Seurat object as .rds.
+
+Set workflow-specific `resources` or command line arguments (CLI) in the workflow profile `workflow/profiles/default.config.yaml`, which supersedes global Snakemake profiles.

config/config.yaml

@@ -2,7 +2,6 @@
 ##### RESOURCES #####
 mem: '32000'
 threads: 1
-partition: 'shortq'
 
 ##### GENERAL #####
 annotation: /path/to/mixscape_seurat_annotation.csv

workflow/Snakefile

@@ -1,11 +1,16 @@
+
+##### global workflow dependencies #####
+conda: "envs/global.yaml"
+
 ##### libraries #####
 import os
 import sys
 import pandas as pd
 import yaml
 from snakemake.utils import min_version
 
-min_version("7.15.2")
+##### set minimum snakemake version #####
+min_version("8.20.1")
 
 ##### module name #####
 module_name = "mixscape_seurat"
@@ -27,18 +32,16 @@ rule all:
                                sample=samples),
         prtb_score_plots = expand(os.path.join(result_path,'{sample}','plots','PerturbScore'),
                                  sample=samples),
-        envs = expand(os.path.join(config["result_path"],'envs',module_name,'{env}.yaml'),env=['seurat_mixscape','seurat_lda']),
-        configs = os.path.join(config["result_path"],'configs',module_name,'{}_config.yaml'.format(config["project_name"])),
-        annotations = os.path.join(config["result_path"],'configs',module_name,'{}_annot.csv'.format(config["project_name"])),
+        envs = expand(os.path.join(result_path,'envs','{env}.yaml'),env=['seurat_mixscape','seurat_lda']),
+        configs = os.path.join(result_path,'configs','{}_config.yaml'.format(config["project_name"])),
+        annotations = os.path.join(result_path,'configs','{}_annot.csv'.format(config["project_name"])),
     resources:
         mem_mb=config.get("mem", "8000"),
     threads: config.get("threads", 1)
     log:
         os.path.join("logs","rules","all.log"),
-    params:
-        partition=config.get("partition"),
 
-        
+
 ##### load rules #####
 include: os.path.join("rules", "common.smk")
 include: os.path.join("rules", "mixscape.smk")

workflow/envs/global.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - numpy=2.0.1
+  - pandas=2.2.2

workflow/profiles/default/config.yaml

@@ -0,0 +1,3 @@
+default-resources:
+    slurm_partition: shortq
+    slurm_extra: "'--qos=shortq'"

workflow/rules/envs_export.smk

@@ -1,20 +1,18 @@
 # one rule per used conda environment to document the exact versions and builds of the used software        
 rule env_export:
     output:
-        report(os.path.join(config["result_path"],'envs','mixscape_seurat','{env}.yaml'),
+        report(os.path.join(result_path,'envs','{env}.yaml'),
                       caption="../report/software.rst", 
                       category="Software", 
-                      subcategory="{}_mixscape_seurat".format(config["project_name"])
+                      subcategory="{}_{}".format(config["project_name"],module_name)
                      ),
     conda:
         "../envs/{env}.yaml"
     resources:
-        mem_mb=1000, #config.get("mem", "16000"),
+        mem_mb=1000,
     threads: config.get("threads", 1)
     log:
         os.path.join("logs","rules","env_{env}.log"),
-    params:
-        partition=config.get("partition"),
     shell:
         """
         conda env export > {output}
@@ -23,18 +21,16 @@ rule env_export:
 # add configuration files to report
 rule config_export:
     output:
-        configs = report(os.path.join(config["result_path"],'configs','mixscape_seurat','{}_config.yaml'.format(config["project_name"])), 
+        configs = report(os.path.join(result_path,'configs','{}_config.yaml'.format(config["project_name"])), 
                          caption="../report/configs.rst", 
                          category="Configuration", 
-                         subcategory="{}_mixscape_seurat".format(config["project_name"])
+                         subcategory="{}_{}".format(config["project_name"],module_name)
                         )
     resources:
-        mem_mb=1000, #config.get("mem", "16000"),
+        mem_mb=1000,
     threads: config.get("threads", 1)
     log:
         os.path.join("logs","rules","config_export.log"),
-    params:
-        partition=config.get("partition"),
     run:
         with open(output["configs"], 'w') as outfile:
             yaml.dump(config, outfile)
@@ -44,18 +40,16 @@ rule annot_export:
     input:
         config["annotation"],
     output:
-        annot = report(os.path.join(config["result_path"],'configs','mixscape_seurat','{}_annot.csv'.format(config["project_name"])), 
+        annot = report(os.path.join(result_path,'configs','{}_annot.csv'.format(config["project_name"])), 
                          caption="../report/configs.rst", 
                          category="Configuration", 
-                         subcategory="{}_mixscape_seurat".format(config["project_name"])
+                         subcategory="{}_{}".format(config["project_name"],module_name)
                         )
     resources:
-        mem_mb=1000, #config.get("mem_small", "16000"),
+        mem_mb=1000,
     threads: config.get("threads", 1)
     log:
         os.path.join("logs","rules","annot_export.log"),
-    params:
-        partition=config.get("partition"),
     shell:
         """
         cp {input} {output}

workflow/rules/mixscape.smk

@@ -25,8 +25,6 @@ rule mixscape:
         "../envs/seurat_mixscape.yaml"
     log:
         os.path.join("logs","rules","mixscape_{sample}.log"),
-    params:
-        partition=config.get("partition"),
     script:
         "../scripts/mixscape.R"
 
@@ -56,7 +54,5 @@ rule lda:
         "../envs/seurat_lda.yaml"
     log:
         os.path.join("logs","rules","lda_{sample}.log"),
-    params:
-        partition=config.get("partition"),
     script:
         "../scripts/lda.R"

workflow/rules/visualize.smk

@@ -41,7 +41,5 @@ rule visualize:
         "../envs/seurat_mixscape.yaml"
     log:
         os.path.join("logs","rules","visualize_{sample}.log"),
-    params:
-        partition=config.get("partition"),
     script:
         "../scripts/visualize.R"