undo pending assay table changes, add suspect log2fc table output to vv dge (#147)

Author: torres-alexis

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/bin/update_assay_table.py

@@ -713,7 +713,7 @@ def add_trimmed_data_column(df, glds_prefix, runsheet_df=None):
     Returns:
         The modified dataframe
     """
-    column_name = "Parameter Value[Trimmed Sequence Data/Fastq]"
+    column_name = "Parameter Value[Trimmed Sequence Data]"
     alternative_names = [
         "Parameter Value[Trimmed Sequence Data Fastqc File]"
     ]
@@ -882,8 +882,8 @@ def add_rseqc_multiqc_reports_column(df, glds_prefix, assay_suffix):
 
 def add_raw_counts_data_column(df, glds_prefix, assay_suffix, mode=""):
     """Add the Raw Counts Data column to the dataframe."""
-    column_name = "Parameter Value[Raw Counts Data/Count Data]"
-    alternative_names = ["Parameter Value[Raw Counts Data]"]
+    column_name = "Parameter Value[Raw Counts Data]"
+    alternative_names = []
 
     # Find the sample name column in the assay table
     sample_col = next((col for col in df.columns if 'Sample Name' in col), None)
@@ -946,7 +946,7 @@ def add_raw_counts_data_column(df, glds_prefix, assay_suffix, mode=""):
                 values.append(",".join(rsem_files))
 
     # Add the column to the dataframe
-    df = update_column(df, column_name, values, alternative_names)
+    df = update_column(df, column_name, values)
 
     return df
 
@@ -1068,8 +1068,8 @@ def add_differential_expression_column(df, glds_prefix, assay_suffix):
 def add_aligned_sequence_data_column(df, glds_prefix, runsheet_df=None, mode=""):
     """Add the aligned sequence data column to the dataframe."""
     # Title Case column name
-    column_name = "Parameter Value[Aligned Sequence Data/Aligned Data]"
-    alternative_names = ["Parameter Value[Aligned Sequence Data]"]
+    column_name = "Parameter Value[Aligned Sequence Data]"
+    alternative_names = []
 
     # Find the sample name column in the assay table
     sample_col = next((col for col in df.columns if 'Sample Name' in col), None)
@@ -1127,7 +1127,7 @@ def add_aligned_sequence_data_column(df, glds_prefix, runsheet_df=None, mode="")
             values.append(",".join(files))
 
     # Add the column to the dataframe
-    df = update_column(df, column_name, values, alternative_names)
+    df = update_column(df, column_name, values)
 
     return df