Merge pull request #267 from hydra-genetics/Smeds-patch-2

fix: minor bug fixes
hydra-genetics · Jun 2, 2023 · 9d8dc59 · 9d8dc59
2 parents 386c961 + 6ff2d9c
commit 9d8dc59
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Showing 3 changed files with 8 additions and 7 deletions.
diff --git a/hydra_genetics/commands/prep_pipeline_env.py b/hydra_genetics/commands/prep_pipeline_env.py
@@ -77,7 +77,7 @@ def container_path_update(configfile, new_configfile, singularity_cache_path):
     help="path to update config file",
 )
 @click.option(
-    "--reference-paths",
+    "--reference-path",
     multiple=True,
     prompt="path",
     required=True,
@@ -87,7 +87,7 @@ def container_path_update(configfile, new_configfile, singularity_cache_path):
         " file and replace all occurrences of oldpath with new path"
     ),
 )
-def reference_path_update(configfile, new_configfile, reference_paths):
+def reference_path_update(configfile, new_configfile, reference_path):
     def process_yaml_data(yaml_data, reference_path):
         for key in yaml_data:
             if isinstance(yaml_data[key], dict):
@@ -98,15 +98,15 @@ def process_yaml_data(yaml_data, reference_path):
                         if old_path in yaml_data[key]:
                             yaml_data[key] = yaml_data[key].replace(old_path, new_path)
         return yaml_data
-    reference_paths = [r.split(":") for r in reference_paths]
+    reference_paths = [r.split(":") for r in reference_path]
     with open(configfile, "r") as stream:
         try:
             yaml_data = yaml.safe_load(stream)
         except yaml.YAMLError as exc:
             print(exc)
             exit(1)
 
-    yaml_data = process_yaml_data(yaml_data, reference_path)
+    yaml_data = process_yaml_data(yaml_data, reference_paths)
 
     with open(new_configfile, 'w') as file:
         for key, value in yaml_data.items():

diff --git a/hydra_genetics/commands/references.py b/hydra_genetics/commands/references.py
@@ -74,14 +74,15 @@ def is_file_or_folder(possible_file):
 
         extension = pathlib.Path(possible_file)
         # docker container aren't files
-        if ":" in possible_file:
+        if ":" in possible_file or possible_file.endswith(".sif"):
             return False
         # Skip files that are configured per analysis/site
         if possible_file.endswith("samples.tsv") \
            or possible_file.endswith("resources.yaml") \
            or possible_file.endswith("units.tsv") \
            or possible_file.endswith("output_list.yaml") \
-           or possible_file.endswith("output_list.json"):
+           or possible_file.endswith("output_list.json") \
+           or possible_file.endswith("snakemake-wrappers"):
             logging.debug(f"Ignore: {possible_file}")
             return False
         # If a extension can be found we consider it as a file

diff --git a/hydra_genetics/utils/io/reference.py b/hydra_genetics/utils/io/reference.py
@@ -128,7 +128,7 @@ def track_files(path, file_list=[], not_found_in_config=[], found=[]):
             else:
                 if 'checksum' not in item:
                     counter_pass += 1
-                    logging.debug(f"{item[path]} found, no checksum validation!")
+                    logging.debug(f"{item['path']} found, no checksum validation!")
                 else:
                     calculated_md5 = hashlib.md5(open(file_path, 'rb').read()).hexdigest()
                     if not calculated_md5 == item['checksum']: