Try to sanitise samplenames in auto-gen pipeline sheets

SPAAM-community · Apr 23, 2024 · 226feed · 226feed
1 parent 7a831c5
commit 226feed
Showing 1 changed file with 12 additions and 0 deletions.
diff --git a/AMDirT/core/__init__.py b/AMDirT/core/__init__.py
@@ -241,6 +241,9 @@ def prepare_eager_table(
         supported_archives (list): list of supported archives
     """
 
+    ## Reduce risk of filename incompatible characters in sample names
+    libraries["sample_name"] = libraries["sample_name"].replace(" ", "_").replace("/", "_")
+
     libraries["Colour_Chemistry"] = libraries["instrument_model"].apply(
         get_colour_chemistry
     )
@@ -299,6 +302,9 @@ def prepare_mag_table(
         supported_archives (list): list of supported archives
     """
 
+    ## Reduce risk of filename incompatible characters in sample names
+    libraries["sample_name"] = libraries["sample_name"].replace(" ", "_").replace("/", "_")
+
     # Create a DataFrame for "SINGLE" values
     single_libraries = libraries[libraries["library_layout"] == "SINGLE"]
 
@@ -386,6 +392,9 @@ def prepare_taxprofiler_table(
         supported_archives (list): list of supported archives
     """
 
+    ## Reduce risk of filename incompatible characters in sample names
+    libraries["sample_name"] = libraries["sample_name"].replace(" ", "_").replace("/", "_")
+
     libraries["fastq_1"] = libraries["download_links"].apply(
         get_filename, orientation="fwd"
     )
@@ -457,6 +466,9 @@ def prepare_aMeta_table(
         supported_archives (list): list of supported archives
     """
 
+    ## Reduce risk of filename incompatible characters in sample names
+    libraries["sample_name"] = libraries["sample_name"].replace(" ", "_").replace("/", "_")
+
     libraries["Colour_Chemistry"] = libraries["instrument_model"].apply(
         get_colour_chemistry
     )