From 71ed0e74015659782ce6d69eeabebb6f6753777b Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Tue, 7 Dec 2021 11:21:57 +0100
Subject: [PATCH] change params names

---
 raw_inputs/raw_fast5_dir.py                        | 2 +-
 tools/guppy/guppy.rule.snakefile                   | 4 ++--
 tools/mitoz_annotate/mitoz_annotate.rule.snakefile | 8 ++++----
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/raw_inputs/raw_fast5_dir.py b/raw_inputs/raw_fast5_dir.py
index d44e0818..10ca3e19 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 9439fb74..3d0b459e 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 7637de6e..5c4c0f55 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()
-- 
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