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kedhammar · Dec 1, 2023 · a300835 · a300835
1 parent 29b34b5
commit a300835
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Showing 6 changed files with 17 additions and 22 deletions.
diff --git a/scripts/comments_to_running_notes.py b/scripts/comments_to_running_notes.py
@@ -163,9 +163,7 @@ def main(lims, args):
             comments = pro.udf["Comments"].encode("utf-8")
         note = "Comment from {} ({}) : \n{}".format(
             pro.type.name,
-            "[LIMS]({}/clarity/work-details/{})".format(
-                BASEURI, pro.id.split("-")[1]
-            ),
+            "[LIMS]({}/clarity/work-details/{})".format(BASEURI, pro.id.split("-")[1]),
             comments,
         )
         noteobj["note"] = note

diff --git a/scripts/copy_reference_genome.py b/scripts/copy_reference_genome.py
@@ -85,9 +85,9 @@ def check_udf_is_defined(projects, udf):
             filtered_projects.append(project)
         else:
             logging.warning(
-                (
-                    "Found project with id {} with {} " "undefined/blank, exiting"
-                ).format(project.id, udf)
+                ("Found project with id {} with {} " "undefined/blank, exiting").format(
+                    project.id, udf
+                )
             )
             incorrect_projects.append(project)
     return filtered_projects, incorrect_projects

diff --git a/scripts/molar_concentration.py b/scripts/molar_concentration.py
@@ -45,8 +45,7 @@ def check_udf_is_defined(artifacts, udf):
         else:
             logging.warning(
                 (
-                    "Found artifact for sample {} with {} "
-                    "undefined/blank, skipping"
+                    "Found artifact for sample {} with {} " "undefined/blank, skipping"
                 ).format(artifact.samples[0].name, udf)
             )
             incorrect_artifacts.append(artifact)
@@ -71,8 +70,7 @@ def check_udf_has_value(artifacts, udf, value):
             incorrect_artifacts.append(artifact)
             logging.warning(
                 (
-                    "Filtered out artifact for sample: {}"
-                    ", due to undefined/blank {}"
+                    "Filtered out artifact for sample: {}" ", due to undefined/blank {}"
                 ).format(artifact.samples[0].name, udf)
             )
 

diff --git a/scripts/qc_amount_calculation.py b/scripts/qc_amount_calculation.py
@@ -106,8 +106,7 @@ def check_udf_is_defined(artifacts, udf):
         else:
             logging.warning(
                 (
-                    "Found artifact for sample {} with {} "
-                    "undefined/blank, skipping"
+                    "Found artifact for sample {} with {} " "undefined/blank, skipping"
                 ).format(artifact.samples[0].name, udf)
             )
             incorrect_artifacts.append(artifact)
@@ -132,8 +131,7 @@ def check_udf_has_value(artifacts, udf, value):
             incorrect_artifacts.append(artifact)
             logging.warning(
                 (
-                    "Filtered out artifact for sample: {}"
-                    ", due to undefined/blank {}"
+                    "Filtered out artifact for sample: {}" ", due to undefined/blank {}"
                 ).format(artifact.samples[0].name, udf)
             )
 

diff --git a/scripts/quantit_set_QC.py b/scripts/quantit_set_QC.py
@@ -60,9 +60,9 @@ def __init__(self, process):
         self.result_files = process.result_files()
         self.udfs = dict(list(process.udf.items()))
         self.required_udfs = {
-                "Allowed %CV of duplicates",
-                "Saturation threshold of fluorescence intensity",
-                "Minimum required concentration (ng/ul)",
+            "Allowed %CV of duplicates",
+            "Saturation threshold of fluorescence intensity",
+            "Minimum required concentration (ng/ul)",
         }
         self.abstract = []
         self.missing_udfs = []

diff --git a/scripts/undemultiplexed_index.py b/scripts/undemultiplexed_index.py
@@ -149,9 +149,9 @@ def _get_file_path(self, cont_name):
             path_id = cont_name
         try:
             self.file_path = glob.glob(
-                    "/srv/ngi-nas-ns/{}/*{}/Unaligned/" "Basecall_Stats_*/".format(
-                        data_folder, path_id
-                    )
+                "/srv/ngi-nas-ns/{}/*{}/Unaligned/" "Basecall_Stats_*/".format(
+                    data_folder, path_id
+                )
             )[0]
         except:
             sys.exit("Failed to get file path")
@@ -253,8 +253,9 @@ def run_QC(self):
             if self.high_lane_yield:
                 self.high_lane_yield = ", ".join(list(set(self.high_lane_yield)))
                 warn = (
-                    "{} High total yield of unexpected index on lane(s): "
-                    "{}.".format(warn, self.high_lane_yield)
+                    "{} High total yield of unexpected index on lane(s): " "{}.".format(
+                        warn, self.high_lane_yield
+                    )
                 )
             warn = warn + "Please check the Metrics file!"
             self.abstract.insert(0, warn)