diff --git a/raw_inputs/raw_fast5_dir.py b/raw_inputs/raw_fast5_dir.py
index d44e0818e871f36626318139c5bf47bae439a3c1..10ca3e19c2033c49dd54624bb694ded68f0b8169 100755
--- a/raw_inputs/raw_fast5_dir.py
+++ b/raw_inputs/raw_fast5_dir.py
@@ -8,7 +8,7 @@ def raw_fast5_dir(results_dir, input_dir):
     out["fast5_dir"] = input_dir
 
     out["samples"] = ""
-
+    out["sample_suffix"] = "Minion"
     return(out)
 
 #print(raw_fast5_dir(sys.argv[1],sys.argv[2],sys.argv[3]))
\ No newline at end of file
diff --git a/tools/guppy/guppy.rule.snakefile b/tools/guppy/guppy.rule.snakefile
index 9439fb7439b16d468f2de30cb459ac239f192b80..3d0b459ed9ccbffc8ca55842411944c7141d5675 100644
--- a/tools/guppy/guppy.rule.snakefile
+++ b/tools/guppy/guppy.rule.snakefile
@@ -21,8 +21,8 @@ rule <step_name>__guppy:
             "-i {input.fast5_dir} "+
             "-s {params.output_dir} "+
             "-c /opt/biotools/ont-guppy/data/{params.config_file} " +
-            "--gpu_num_callers {params.gpu_num_callers} " +
-            "--guppy_gpu_runners_per_device {params.gpu_runners_per_device} ; "
+            "--num_callers {params.gpu_num_callers} " +
+            "--gpu_runners_per_device {params.gpu_runners_per_device} ; "
             "cat {params.output_dir}/pass/*.fastq.gz > {params.output_dir}/guppy_pass.fq.gz ; "
             "rm -f {params.output_dir}/pass/*.fastq.gz; "
             "cat {params.output_dir}/fail/*.fastq.gz > {params.output_dir}/guppy_fail.fastq.gz ; "            
diff --git a/tools/mitoz_annotate/mitoz_annotate.rule.snakefile b/tools/mitoz_annotate/mitoz_annotate.rule.snakefile
index 7637de6ee48d9d0bb7d94c035e8b62ebda9fb888..5c4c0f5547bf45b956dd9d49846d9cec5b55a5d0 100755
--- a/tools/mitoz_annotate/mitoz_annotate.rule.snakefile
+++ b/tools/mitoz_annotate/mitoz_annotate.rule.snakefile
@@ -1,5 +1,5 @@
-if config["SeOrPe"] == "SE":
-
+#if config["SeOrPe"] == "SE": #SeOrPe will not be defined if we are using fast5_dir followed by guppy as the source of reads
+if "<step_name>__mitoz_annotate_SE_inputs" in globals():
     rule <step_name>__mitoz_annotate_SE:
         input:
             **<step_name>__mitoz_annotate_SE_inputs()
@@ -55,8 +55,8 @@ if config["SeOrPe"] == "SE":
             "rm {params.results_dir}/reads_R1{params.sample_suffix} "
 
 
-elif config["SeOrPe"] == "PE":
-
+#elif config["SeOrPe"] == "PE":
+elif if "<step_name>__mitoz_annotate_PE_inputs" in globals():
     rule <step_name>__mitoz_annotate_PE:
         input:
             **<step_name>__mitoz_annotate_PE_inputs()