Automatically determine DEseq2 threads based on Twitter note from Mik…

…e Love.

config.yaml

@@ -23,6 +23,3 @@ params:
   star: ""
   cutadapt-se: ""
   cutadapt-pe: ""
-  deseq2:
-    # if you have many samples or conditions, you can use more than 1 thread here.
-    threads: 1

rules/diffexp.smk

@@ -9,6 +9,12 @@ rule count_matrix:
         "../scripts/count-matrix.py"
 
 
+def get_deseq2_threads(wildcards=None):
+    # https://twitter.com/mikelove/status/918770188568363008
+    few_coeffs = False if wildcards is None else len(get_contrast(wildcards)) < 10
+    return 1 if len(samples) < 100 or few_coeffs else 6
+
+
 rule deseq2_init:
     input:
         counts="counts/all.tsv",
@@ -19,7 +25,7 @@ rule deseq2_init:
         "../envs/deseq2.yaml"
     log:
         "logs/deseq2/init.log"
-    threads: config["params"]["deseq2"]["threads"]
+    threads: get_deseq2_threads(None)
     script:
         "../scripts/deseq2-init.R"
 
@@ -55,6 +61,6 @@ rule deseq2:
         "../envs/deseq2.yaml"
     log:
         "logs/deseq2/{contrast}.diffexp.log"
-    threads: config["params"]["deseq2"]["threads"]
+    threads: get_deseq2_threads
     script:
         "../scripts/deseq2.R"