remove get_threads( function

frangiPANe/snakefiles/abyss_merge.smk

@@ -30,4 +30,4 @@ rule abyss_merge:
 
             process = subprocess.run(cmd, shell=True, capture_output=True, text=True)
             if process.returncode != 0:
-                raise ValueError(f"Error executing command: {process.stderr}")
\ No newline at end of file
+                raise ValueError(f"Error executing command: {process.stderr}")

frangiPANe/snakefiles/samtools_flagstat.smk

@@ -7,7 +7,7 @@ rule samtools_flagstat:
     log:
         output =  f"{frangipane_obj.path_logs}/stats/flagstat-{{sample_name}}-{{ref_name}}.o",
         error =  f"{frangipane_obj.path_logs}/stats/flagstat-{{sample_name}}-{{ref_name}}.e"
-    threads: get_threads('samtools_flagstat', 1)
+    threads: 1
     message:
         f"""--------------------
 -Running {{rule}}
@@ -28,4 +28,4 @@ rule samtools_flagstat:
         """
         cmd="samtools flagstat -@ {threads} {input.bam_file}";
         (echo $cmd) > {log.output};
-        ($cmd) 1> {output.stat_file} 2> {log.error}"""
\ No newline at end of file
+        ($cmd) 1> {output.stat_file} 2> {log.error}"""

frangiPANe/snakefiles/samtools_view.smk

@@ -10,7 +10,7 @@ rule samtools_view:
         output = f"{frangipane_obj.path_logs}/samtools_view/{{sample_name}}-{{ref_name}}.o"
     params:
         other_options = frangipane_obj.get_config_value("PARAMS","samtools_view"),
-    threads: get_threads('samtools_view', 1)
+    threads: 1
     message:
         f"""--------------------
 -Running {{rule}}
@@ -37,4 +37,4 @@ rule samtools_view:
         
         cmd2="samtools index -@ {threads} {output.bam_file}";
         (echo $cmd2) >> {log.output};
-        ($cmd2) 1>> {log.output} 2>> {log.error}"""
\ No newline at end of file
+        ($cmd2) 1>> {log.output} 2>> {log.error}"""