[mg] minor correction: setup "workflow.cores" as standard number of t…

…hreads

workflow/Snakefile

@@ -1,5 +1,5 @@
-from pathlib import Path
 import pandas as pd
+from pathlib import Path
 import os
 
 # load and validate config stuff
@@ -100,7 +100,7 @@ rule fastp_se:
         length_required = length_required_fastp,
         trim_tail1 = trim_tail1_fastp
     benchmark: log_dir / "benchmark.{sample}.fastp_se.txt"
-    threads: num_threads
+    threads: workflow.cores
     shell:
         '''
         fastp \
@@ -144,7 +144,7 @@ rule fastp_pe:
         right_quality = 15,
         length_required = length_required_fastp
     benchmark: log_dir / "benchmark.{sample}.fastp_pe.txt"
-    threads: num_threads
+    threads: workflow.cores
     shell:
         '''
         fastp \
@@ -263,7 +263,7 @@ if pipeline_config["mode"] == "se":
             folder = "{sample}",
             bam_prefix = lambda wildcards : align_dir / "{}.".format(wildcards.sample)
         benchmark: log_dir / "benchmark.{sample}.STAR_pe.txt"
-        threads: num_threads
+        threads: workflow.cores
         shell:
             '''
             [ -e /tmp/{params.folder} ] && rm -r /tmp/{params.folder}
@@ -304,7 +304,7 @@ if pipeline_config["mode"] == "pe":
         resources:
             load=100
         benchmark: log_dir / "benchmark.{sample}.STAR_se.txt"
-        threads: num_threads
+        threads: workflow.cores
         shell:
             '''
             [ -e /tmp/{params.folder} ] && rm -r /tmp/{params.folder}