diff --git a/staphb_toolkit/workflows/cecret/bin/combine_results.py b/staphb_toolkit/workflows/cecret/bin/combine_results.py
deleted file mode 100644
index 15fe14d..0000000
--- a/staphb_toolkit/workflows/cecret/bin/combine_results.py
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/bin/python
-
-import pandas as pd
-from os.path import exists
-
-pangolin_file='lineage_report.csv'
-nextclade_file='nextclade.csv'
-vadr_file='vadr.csv'
-freyja_file='aggregated-freyja.tsv'
-summary_file='combined_summary.csv'
-
-summary_df = pd.read_csv(summary_file, dtype = str)
-columns = list(summary_df.columns)
-columns.remove('sample_id')
-columns.remove('sample')
-columns.remove('fasta_line')
-
-if exists(vadr_file) :
-    vadr_df = pd.read_csv(vadr_file, dtype = str, usecols = ['name', 'p/f', 'model', 'alerts'], index_col= False)
-    vadr_df=vadr_df.add_prefix('vadr_')
-    vadr_columns = list(vadr_df.columns)
-    vadr_columns.remove('vadr_name')
-    vadr_columns.remove('vadr_p/f')
-
-    summary_df = pd.merge(summary_df, vadr_df, left_on = 'fasta_line', right_on = 'vadr_name', how = 'outer')
-    summary_df['sample_id'].fillna(summary_df['vadr_name'], inplace=True)
-    summary_df['fasta_line'].fillna(summary_df['vadr_name'], inplace=True)
-    summary_df.drop('vadr_name', axis=1, inplace=True)
-    columns = ['vadr_p/f'] + columns + vadr_columns
-
-if exists(nextclade_file) :
-    nextclade_df = pd.read_csv(nextclade_file, sep = ';' , dtype = str, usecols = ['seqName', 'clade', 'qc.overallStatus', 'qc.overallScore'])
-    nextclade_df=nextclade_df.add_prefix('nextclade_')
-    nextclade_columns = list(nextclade_df.columns)
-    nextclade_columns.remove('nextclade_seqName')
-    nextclade_columns.remove('nextclade_clade')
-
-    summary_df = pd.merge(summary_df, nextclade_df, left_on = 'fasta_line', right_on = 'nextclade_seqName', how = 'outer')
-    summary_df['sample_id'].fillna(summary_df['nextclade_seqName'], inplace=True)
-    summary_df['fasta_line'].fillna(summary_df['nextclade_seqName'], inplace=True)
-    summary_df.drop('nextclade_seqName', axis=1, inplace=True)
-    columns = ['nextclade_clade'] + columns + nextclade_columns
-
-if exists(pangolin_file) :
-
-    pangolin_df = pd.read_csv(pangolin_file, dtype = str)
-    pangolin_df=pangolin_df.add_prefix('pangolin_')
-    pangolin_columns = list(pangolin_df.columns)
-    pangolin_columns.remove('pangolin_taxon')
-    pangolin_columns.remove('pangolin_lineage')
-
-    summary_df = pd.merge(summary_df, pangolin_df, left_on = 'fasta_line', right_on = 'pangolin_taxon', how = 'outer')
-    summary_df['sample_id'].fillna(summary_df['pangolin_taxon'], inplace=True)
-    summary_df['fasta_line'].fillna(summary_df['pangolin_taxon'], inplace=True)
-    summary_df.drop('pangolin_taxon', axis=1, inplace=True)
-    columns = ['pangolin_lineage'] + columns + pangolin_columns
-
-if exists(freyja_file) :
-    freyja_df = pd.read_table(freyja_file, dtype = str, sep="\t")
-    freyja_df = freyja_df.add_prefix('freyja_')
-    freyja_df['freyja_Unnamed: 0'] = freyja_df['freyja_Unnamed: 0'].str.replace("_variants.tsv", "")
-    freyja_columns = list(freyja_df.columns)
-    freyja_columns.remove('freyja_Unnamed: 0')
-
-    summary_df = pd.merge(summary_df, freyja_df, left_on = 'sample_id', right_on = 'freyja_Unnamed: 0', how = 'outer')
-    summary_df['sample_id'].fillna(summary_df['freyja_Unnamed: 0'], inplace=True)
-    summary_df['fasta_line'].fillna(summary_df['freyja_Unnamed: 0'], inplace=True)
-    summary_df.drop('freyja_Unnamed: 0', axis=1, inplace=True)
-    columns = columns + freyja_columns
-
-summary_df.to_csv('cecret_results.csv', columns = ['sample_id','sample'] + columns, index=False)