From b8ab85d018e61849cddbfb919eb67d8d25df88c8 Mon Sep 17 00:00:00 2001
From: sreichl <reichl.stephan@gmail.com>
Date: Thu, 23 May 2024 17:33:14 +0200
Subject: [PATCH] cosmetics

---
 config/config.yaml             | 1 +
 workflow/Snakefile             | 2 +-
 workflow/rules/envs_export.smk | 8 ++++----
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/config/config.yaml b/config/config.yaml
index f38159c..6ca5efc 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -17,6 +17,7 @@ test_use: "wilcox"
 min_pct: 0.1
 
 # additional parameter for https://satijalab.org/seurat/reference/findallmarkers
+# Only return markers that have a p-value < return.thresh, or a power > return.thresh (if the test is ROC)
 return_thresh: 1
 
 ##### AGGREGATION #####
diff --git a/workflow/Snakefile b/workflow/Snakefile
index af79076..bb8aab2 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -51,7 +51,7 @@ rule all:
         envs = expand(os.path.join(config["result_path"],'envs',module_name,'{env}.yaml'),env=['seurat','volcanos','ggplot','heatmap']),
         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"])),
-        feature_lists = expand(os.path.join(config["result_path"],'configs','dea_seurat','{feature_list}.txt'), feature_list = feature_lists),
+        feature_lists = expand(os.path.join(config["result_path"],'configs',module_name,'{feature_list}.txt'), feature_list = feature_lists),
     resources:
         mem_mb=config.get("mem", "16000"),
     threads: config.get("threads", 1)
diff --git a/workflow/rules/envs_export.smk b/workflow/rules/envs_export.smk
index e141589..3f64e08 100644
--- a/workflow/rules/envs_export.smk
+++ b/workflow/rules/envs_export.smk
@@ -4,7 +4,7 @@ rule env_export:
         report(os.path.join(config["result_path"],'envs','dea_seurat','{env}.yaml'),
                       caption="../report/software.rst", 
                       category="Software", 
-                      subcategory="{}_dea_seurat".format(config["project_name"])
+                      subcategory="{}_{}".format(config["project_name"], module_name)
                      ),
     conda:
         "../envs/{env}.yaml"
@@ -26,7 +26,7 @@ rule config_export:
         configs = report(os.path.join(config["result_path"],'configs','dea_seurat','{}_config.yaml'.format(config["project_name"])), 
                          caption="../report/configs.rst", 
                          category="Configuration", 
-                         subcategory="{}_dea_seurat".format(config["project_name"])
+                         subcategory="{}_{}".format(config["project_name"], module_name)
                         )
     resources:
         mem_mb=config.get("mem", "16000"),
@@ -37,7 +37,7 @@ rule config_export:
         partition=config.get("partition"),
     run:
         with open(output["configs"], 'w') as outfile:
-            yaml.dump(config, outfile)
+            yaml.dump(config, outfile, sort_keys=False, width=1000, indent=2)
         
 # export used annotation file for documentation and reproducibility         
 rule annot_export:
@@ -47,7 +47,7 @@ rule annot_export:
         annot = report(os.path.join(config["result_path"],'configs','dea_seurat','{}_annot.csv'.format(config["project_name"])), 
                          caption="../report/configs.rst", 
                          category="Configuration", 
-                         subcategory="{}_dea_seurat".format(config["project_name"])
+                         subcategory="{}_{}".format(config["project_name"], module_name)
                         )
     resources:
         mem_mb=1000, #config.get("mem_small", "16000"),