Merge pull request #45 from sanger-pathogens/v0.0.11

Change mlst columns from int64 to string obj
sanger-bentley-group · Aug 3, 2021 · d5be122 · d5be122
2 parents f07cbb6 + 17572c9
commit d5be122
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Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/bin/combine_results.py b/bin/combine_results.py
@@ -68,6 +68,7 @@ def get_all_content(id, sero_file, res_file_inc, res_file_var, mlst_file, surf_t
     mlst['ST'] = mlst['ST'].astype(str)
     st_value = 'ST-' + mlst.iloc[0]['ST']
     mlst.at[0,'ST'] = st_value
+    mlst = mlst.astype(str)
 
     # Clean resistance incidence
     res_inc = pd.read_csv(res_file_inc, sep='\t', lineterminator='\n')

diff --git a/nextflow.config b/nextflow.config
@@ -1,5 +1,5 @@
 // Dependencies docker image
-process.container = 'quay.io/sangerpathogens/gbs-typer-sanger-nf:v0.0.10'
+process.container = 'quay.io/sangerpathogens/gbs-typer-sanger-nf:v0.0.11'
 
 manifest {
     homePage = 'https://github.com/sanger-pathogens/GBS-Typer-sanger-nf'

diff --git a/tests/combine_results_test.py b/tests/combine_results_test.py
@@ -41,13 +41,13 @@ def test_get_all_content(self):
             'Sample_id': {0: '25292_2#85'},
             'cps_type': {0: 'III'},
             'ST': {0: 'ST-1'},
-            'adhP': {0: 1},
-            'pheS': {0: 1},
-            'atr': {0: 2},
-            'glnA': {0: 1},
-            'sdhA': {0: 1},
-            'glcK': {0: 2},
-            'tkt': {0: 2},
+            'adhP': {0: '1'},
+            'pheS': {0: '1'},
+            'atr': {0: '2'},
+            'glnA': {0: '1'},
+            'sdhA': {0: '1'},
+            'glcK': {0: '2'},
+            'tkt': {0: '2'},
             '23S1': {0: 'pos'},
             '23S3': {0: 'pos'},
             'CAT': {0: 'neg'},