From 09efa91d770b332f8cff2b083e940756b6177362 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Thu, 15 Aug 2024 14:50:54 -0400
Subject: [PATCH 01/25] Update locidex container registry

---
 modules/local/locidex/merge/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/locidex/merge/main.nf b/modules/local/locidex/merge/main.nf
index 058d3a3..66ba9a7 100644
--- a/modules/local/locidex/merge/main.nf
+++ b/modules/local/locidex/merge/main.nf
@@ -5,8 +5,8 @@ process LOCIDEX_MERGE {
     label 'process_medium'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'https://depot.galaxyproject.org/singularity/locidex:0.1.1--pyhdfd78af_0' :
-    'quay.io/biocontainers/locidex:0.1.1--pyhdfd78af_0' }"
+    'docker.io/mwells14/locidex:0.2.2' :
+    'docker.io/mwells14/locidex:0.2.2' }"
 
     input:
     path input_values // [file(sample1), file(sample2), file(sample3), etc...]

From 9e820c828c703bff5958cc02f387715768cf9dc8 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Thu, 15 Aug 2024 14:52:43 -0400
Subject: [PATCH 02/25] Update input_assure.py to accomodate the revised
 Locidex mlst.json report format

---
 assets/samplesheet.csv |  6 +++---
 bin/input_assure.py    | 29 ++++++++++++++++++-----------
 conf/test.config       |  2 +-
 3 files changed, 22 insertions(+), 15 deletions(-)

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 82842ce..7438d85 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json
+sample1,/root/working_directory/nml-phac/gasclustering/tests/data/reports/sample1.mlst.json
+sample2,/root/working_directory/nml-phac/gasclustering/tests/data/reports/sample2.mlst.json
+sample3,/root/working_directory/nml-phac/gasclustering/tests/data/reports/sample3.mlst.json
diff --git a/bin/input_assure.py b/bin/input_assure.py
index d99bf2a..7f5d56e 100755
--- a/bin/input_assure.py
+++ b/bin/input_assure.py
@@ -19,18 +19,24 @@ def check_inputs(json_file, sample_id, address, output_error_file, output_json_f
     with open_file(json_file, "rt") as f:
         json_data = json.load(f)
 
+    print(json.dumps(json_data, indent=4))
+
+    # Extract the profile from the json_data
+    profile = json_data.get("data", {}).get("profile", {})
+    # Check for multiple keys in the JSON file and define error message
+    keys = list(profile.keys())
+    original_key = keys[0] if keys else None
+
     # Define a variable to store the match_status (True or False)
-    match_status = sample_id in json_data
+    match_status = sample_id in profile
 
     # Initialize the error message
     error_message = None
 
-    # Check for multiple keys in the JSON file and define error message
-    keys = list(json_data.keys())
-    original_key = keys[0] if keys else None
-
-    if len(keys) == 0:
-        error_message = f"{json_file} is completely empty!"
+    if not keys:
+        error_message = (
+            f"{json_file} is missing the 'profile' section or is completely empty!"
+        )
         print(error_message)
         sys.exit(1)
     elif len(keys) > 1:
@@ -38,11 +44,11 @@ def check_inputs(json_file, sample_id, address, output_error_file, output_json_f
         if not match_status:
             error_message = f"No key in the MLST JSON file ({json_file}) matches the specified sample ID '{sample_id}'. The first key '{original_key}' has been forcefully changed to '{sample_id}' and all other keys have been removed."
             # Retain only the specified sample ID
-            json_data = {sample_id: json_data.pop(original_key)}
+            json_data["data"]["profile"] = {sample_id: profile.pop(original_key)}
         else:
             error_message = f"MLST JSON file ({json_file}) contains multiple keys: {keys}. The MLST JSON file has been modified to retain only the '{sample_id}' entry"
-            # Remove all keys expect the one matching sample_id
-            json_data = {sample_id: json_data[sample_id]}
+            # Retain only the specified sample_id in the profile
+            json_data["data"]["profile"] = {sample_id: profile[sample_id]}
     elif not match_status:
         # Define error message based on meta.address (query or reference)
         if address == "null":
@@ -50,7 +56,8 @@ def check_inputs(json_file, sample_id, address, output_error_file, output_json_f
         else:
             error_message = f"Reference {sample_id} ID and JSON key in {json_file} DO NOT MATCH. The '{original_key}' key in {json_file} has been forcefully changed to '{sample_id}': User should manually check input files to ensure correctness."
         # Update the JSON file with the new sample ID
-        json_data[sample_id] = json_data.pop(original_key)
+        json_data["data"]["profile"] = {sample_id: profile.pop(original_key)}
+        json_data["data"]["sample_name"] = sample_id
 
     # Write file containing relevant error messages
     if error_message:
diff --git a/conf/test.config b/conf/test.config
index 51549ed..b0679a2 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '1.h'
 
     // Input data
-    input  = 'https://raw.githubusercontent.com/phac-nml/gasclustering/dev/assets/samplesheet.csv'
+    input  = "${projectDir}/assets/samplesheet.csv"
 }
 
 

From 29debe1722bb2d7c8c9dbc47c0adfe554198c34e Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Thu, 15 Aug 2024 14:53:34 -0400
Subject: [PATCH 03/25] Update test data (reports and samplesheets) to
 accomodate the revised Locidex mlst.json report format

---
 .../case-hamming/sample1.mlst.subtyping.json  | 22 +++++++++++++++----
 .../case-hamming/sample2.mlst.subtyping.json  | 22 +++++++++++++++----
 .../case-hamming/sample3.mlst.subtyping.json  | 22 +++++++++++++++----
 .../sample1.mlst.subtyping.json               | 22 +++++++++++++++----
 .../sample2.mlst.subtyping.json               | 22 +++++++++++++++----
 .../sample3-more-missing.mlst.subtyping.json  | 22 +++++++++++++++----
 .../sample3.mlst.subtyping.json               | 22 +++++++++++++++----
 tests/data/reports/sample1.mlst.json          | 22 +++++++++++++++----
 tests/data/reports/sample2.mlst.json          | 22 +++++++++++++++----
 tests/data/reports/sample3.mlst.json          | 22 +++++++++++++++----
 .../data/samplesheets/samplesheet-hamming.csv |  6 ++---
 .../samplesheets/samplesheet-hash-missing.csv |  6 ++---
 .../samplesheet-hash-more-missing.csv         |  6 ++---
 .../samplesheet-little-metadata.csv           |  6 ++---
 .../samplesheet-mismatched-ids.csv            |  6 ++---
 .../samplesheets/samplesheet-no-metadata.csv  |  6 ++---
 .../samplesheet-partial-mismatched-ids.csv    |  6 ++---
 tests/data/samplesheets/samplesheet-tabs.csv  |  6 ++---
 tests/data/samplesheets/samplesheet1.csv      |  6 ++---
 19 files changed, 207 insertions(+), 67 deletions(-)

diff --git a/tests/data/reports/case-hamming/sample1.mlst.subtyping.json b/tests/data/reports/case-hamming/sample1.mlst.subtyping.json
index 01bc774..63a71b4 100644
--- a/tests/data/reports/case-hamming/sample1.mlst.subtyping.json
+++ b/tests/data/reports/case-hamming/sample1.mlst.subtyping.json
@@ -1,7 +1,21 @@
 {
-    "sample1": {
-        "l1": "1",
-        "l2": "1",
-        "l3": "1"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample1",
+        "profile": {
+            "sample1": {
+                "l1": "1",
+                "l2": "1",
+                "l3": "1"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/reports/case-hamming/sample2.mlst.subtyping.json b/tests/data/reports/case-hamming/sample2.mlst.subtyping.json
index 1e8b0b2..704bcfe 100644
--- a/tests/data/reports/case-hamming/sample2.mlst.subtyping.json
+++ b/tests/data/reports/case-hamming/sample2.mlst.subtyping.json
@@ -1,7 +1,21 @@
 {
-    "sample2": {
-        "l1": "1",
-        "l2": "2",
-        "l3": "1"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample2",
+        "profile": {
+            "sample2": {
+                "l1": "1",
+                "l2": "2",
+                "l3": "1"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/reports/case-hamming/sample3.mlst.subtyping.json b/tests/data/reports/case-hamming/sample3.mlst.subtyping.json
index bec5935..7e8d7f8 100644
--- a/tests/data/reports/case-hamming/sample3.mlst.subtyping.json
+++ b/tests/data/reports/case-hamming/sample3.mlst.subtyping.json
@@ -1,7 +1,21 @@
 {
-    "sample3": {
-        "l1": "2",
-        "l2": "1",
-        "l3": "2"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample3",
+        "profile": {
+            "sample3": {
+                "l1": "2",
+                "l2": "1",
+                "l3": "2"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json b/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json
index e559003..eb8c116 100644
--- a/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json
+++ b/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json
@@ -1,7 +1,21 @@
 {
-    "sample1": {
-        "l1": "b026324c6904b2a9cb4b88d6d61c81d1",
-        "l2": "b026324c6904b2a9cb4b88d6d61c81d1",
-        "l3": "b026324c6904b2a9cb4b88d6d61c81d1"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample1",
+        "profile": {
+            "sample1": {
+                "l1": "b026324c6904b2a9cb4b88d6d61c81d1",
+                "l2": "b026324c6904b2a9cb4b88d6d61c81d1",
+                "l3": "b026324c6904b2a9cb4b88d6d61c81d1"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json b/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json
index 06148ce..ee75b74 100644
--- a/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json
+++ b/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json
@@ -1,7 +1,21 @@
 {
-    "sample2": {
-        "l1": "-",
-        "l2": "26ab0db90d72e28ad0ba1e22ee510510",
-        "l3": "b026324c6904b2a9cb4b88d6d61c81d1"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample2",
+        "profile": {
+            "sample2": {
+                "l1": "-",
+                "l2": "26ab0db90d72e28ad0ba1e22ee510510",
+                "l3": "b026324c6904b2a9cb4b88d6d61c81d1"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/reports/case-hash-missing/sample3-more-missing.mlst.subtyping.json b/tests/data/reports/case-hash-missing/sample3-more-missing.mlst.subtyping.json
index 7546de9..0bf1372 100644
--- a/tests/data/reports/case-hash-missing/sample3-more-missing.mlst.subtyping.json
+++ b/tests/data/reports/case-hash-missing/sample3-more-missing.mlst.subtyping.json
@@ -1,7 +1,21 @@
 {
-    "sample3": {
-        "l1": "-",
-        "l2": "-",
-        "l3": "26ab0db90d72e28ad0ba1e22ee510510"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample3",
+        "profile": {
+            "sample3": {
+                "l1": "-",
+                "l2": "-",
+                "l3": "26ab0db90d72e28ad0ba1e22ee510510"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/reports/case-hash-missing/sample3.mlst.subtyping.json b/tests/data/reports/case-hash-missing/sample3.mlst.subtyping.json
index a0f0259..fe8441d 100644
--- a/tests/data/reports/case-hash-missing/sample3.mlst.subtyping.json
+++ b/tests/data/reports/case-hash-missing/sample3.mlst.subtyping.json
@@ -1,7 +1,21 @@
 {
-    "sample3": {
-        "l1": "-",
-        "l2": "b026324c6904b2a9cb4b88d6d61c81d1",
-        "l3": "26ab0db90d72e28ad0ba1e22ee510510"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample3",
+        "profile": {
+            "sample3": {
+                "l1": "-",
+                "l2": "b026324c6904b2a9cb4b88d6d61c81d1",
+                "l3": "26ab0db90d72e28ad0ba1e22ee510510"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/reports/sample1.mlst.json b/tests/data/reports/sample1.mlst.json
index 01bc774..63a71b4 100644
--- a/tests/data/reports/sample1.mlst.json
+++ b/tests/data/reports/sample1.mlst.json
@@ -1,7 +1,21 @@
 {
-    "sample1": {
-        "l1": "1",
-        "l2": "1",
-        "l3": "1"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample1",
+        "profile": {
+            "sample1": {
+                "l1": "1",
+                "l2": "1",
+                "l3": "1"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/reports/sample2.mlst.json b/tests/data/reports/sample2.mlst.json
index 7c0426c..3d9ee23 100644
--- a/tests/data/reports/sample2.mlst.json
+++ b/tests/data/reports/sample2.mlst.json
@@ -1,7 +1,21 @@
 {
-    "sample2": {
-        "l1": "1",
-        "l2": "1",
-        "l3": "1"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample2",
+        "profile": {
+            "sample2": {
+                "l1": "1",
+                "l2": "1",
+                "l3": "1"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/reports/sample3.mlst.json b/tests/data/reports/sample3.mlst.json
index 43ea3c7..d57ee75 100644
--- a/tests/data/reports/sample3.mlst.json
+++ b/tests/data/reports/sample3.mlst.json
@@ -1,7 +1,21 @@
 {
-    "sample3": {
-        "l1": "1",
-        "l2": "1",
-        "l3": "2"
+    "db_info": {},
+    "parameters": {
+        "mode": "normal",
+        "min_match_ident": 100,
+        "min_match_cov": 100,
+        "max_ambiguous": 0,
+        "max_internal_stops": 0
+    },
+    "data": {
+        "sample_name": "sample3",
+        "profile": {
+            "sample3": {
+                "l1": "1",
+                "l2": "1",
+                "l3": "2"
+            }
+        },
+        "seq_data": {}
     }
 }
diff --git a/tests/data/samplesheets/samplesheet-hamming.csv b/tests/data/samplesheets/samplesheet-hamming.csv
index d18a69c..14f2469 100644
--- a/tests/data/samplesheets/samplesheet-hamming.csv
+++ b/tests/data/samplesheets/samplesheet-hamming.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hamming/sample1.mlst.subtyping.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hamming/sample2.mlst.subtyping.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hamming/sample3.mlst.subtyping.json,,,,,,,,
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample1.mlst.subtyping.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/update/input_assure/reports/case-hamming/sample2.mlst.subtyping.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/update/input_assure/reports/case-hamming/sample3.mlst.subtyping.json,,,,,,,,
diff --git a/tests/data/samplesheets/samplesheet-hash-missing.csv b/tests/data/samplesheets/samplesheet-hash-missing.csv
index 9355c3d..6ad5929 100644
--- a/tests/data/samplesheets/samplesheet-hash-missing.csv
+++ b/tests/data/samplesheets/samplesheet-hash-missing.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hash-missing/sample3.mlst.subtyping.json,,,,,,,,
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample3.mlst.subtyping.json,,,,,,,,
diff --git a/tests/data/samplesheets/samplesheet-hash-more-missing.csv b/tests/data/samplesheets/samplesheet-hash-more-missing.csv
index ae223fb..37f051f 100644
--- a/tests/data/samplesheets/samplesheet-hash-more-missing.csv
+++ b/tests/data/samplesheets/samplesheet-hash-more-missing.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/profile_dists/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/profile_dists/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/profile_dists/tests/data/reports/case-hash-missing/sample3-more-missing.mlst.subtyping.json,,,,,,,,
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample3-more-missing.mlst.subtyping.json,,,,,,,,
diff --git a/tests/data/samplesheets/samplesheet-little-metadata.csv b/tests/data/samplesheets/samplesheet-little-metadata.csv
index 3e721de..052b4b3 100644
--- a/tests/data/samplesheets/samplesheet-little-metadata.csv
+++ b/tests/data/samplesheets/samplesheet-little-metadata.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,,,,1.4,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,3.1,3.2,,,,,,3.8
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,,,,1.4,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,3.1,3.2,,,,,,3.8
diff --git a/tests/data/samplesheets/samplesheet-mismatched-ids.csv b/tests/data/samplesheets/samplesheet-mismatched-ids.csv
index 632768d..6df7315 100644
--- a/tests/data/samplesheets/samplesheet-mismatched-ids.csv
+++ b/tests/data/samplesheets/samplesheet-mismatched-ids.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sampleA,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
-sampleB,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
-sampleC,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
+sampleA,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
+sampleB,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
+sampleC,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
diff --git a/tests/data/samplesheets/samplesheet-no-metadata.csv b/tests/data/samplesheets/samplesheet-no-metadata.csv
index 9d67864..5f4d2ca 100644
--- a/tests/data/samplesheets/samplesheet-no-metadata.csv
+++ b/tests/data/samplesheets/samplesheet-no-metadata.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,,,,,,,,
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,,,,,,,,
diff --git a/tests/data/samplesheets/samplesheet-partial-mismatched-ids.csv b/tests/data/samplesheets/samplesheet-partial-mismatched-ids.csv
index d5d42f0..cd0655d 100644
--- a/tests/data/samplesheets/samplesheet-partial-mismatched-ids.csv
+++ b/tests/data/samplesheets/samplesheet-partial-mismatched-ids.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sampleA,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
-sampleB,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
+sampleA,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
+sampleB,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
diff --git a/tests/data/samplesheets/samplesheet-tabs.csv b/tests/data/samplesheets/samplesheet-tabs.csv
index 56b4243..4408655 100644
--- a/tests/data/samplesheets/samplesheet-tabs.csv
+++ b/tests/data/samplesheets/samplesheet-tabs.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,a	b,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,,,,a	b,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,,,,,,,,a	b
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,a	b,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,,,,a	b,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,,,,,,,,a	b
diff --git a/tests/data/samplesheets/samplesheet1.csv b/tests/data/samplesheets/samplesheet1.csv
index 3200344..f78cff3 100644
--- a/tests/data/samplesheets/samplesheet1.csv
+++ b/tests/data/samplesheets/samplesheet1.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8

From 2cb48888af92d86cca9bfba6b533ba3871d938f3 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Thu, 15 Aug 2024 14:58:57 -0400
Subject: [PATCH 04/25] Update paths to mlst files in samplesheet.csv

---
 assets/samplesheet.csv | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 7438d85..b283ed7 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles
-sample1,/root/working_directory/nml-phac/gasclustering/tests/data/reports/sample1.mlst.json
-sample2,/root/working_directory/nml-phac/gasclustering/tests/data/reports/sample2.mlst.json
-sample3,/root/working_directory/nml-phac/gasclustering/tests/data/reports/sample3.mlst.json
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json

From cc1444b9ee317a373e356e24cea0d7a70a9c3c1e Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Thu, 15 Aug 2024 16:01:20 -0400
Subject: [PATCH 05/25] Fixed error in samplesheet

---
 tests/data/samplesheets/samplesheet-hamming.csv | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/data/samplesheets/samplesheet-hamming.csv b/tests/data/samplesheets/samplesheet-hamming.csv
index 14f2469..0526692 100644
--- a/tests/data/samplesheets/samplesheet-hamming.csv
+++ b/tests/data/samplesheets/samplesheet-hamming.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
 sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample1.mlst.subtyping.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/update/input_assure/reports/case-hamming/sample2.mlst.subtyping.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/update/input_assure/reports/case-hamming/sample3.mlst.subtyping.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample3.mlst.subtyping.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample3.mlst.subtyping.json,,,,,,,,

From 9a87a2b7670e52925fe11d4b703c710f006b810b Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Fri, 16 Aug 2024 11:01:30 -0400
Subject: [PATCH 06/25] Fixed typo

---
 tests/data/samplesheets/samplesheet-hamming.csv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/data/samplesheets/samplesheet-hamming.csv b/tests/data/samplesheets/samplesheet-hamming.csv
index 0526692..df78ac4 100644
--- a/tests/data/samplesheets/samplesheet-hamming.csv
+++ b/tests/data/samplesheets/samplesheet-hamming.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
 sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample1.mlst.subtyping.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample3.mlst.subtyping.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample2.mlst.subtyping.json,,,,,,,,
 sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample3.mlst.subtyping.json,,,,,,,,

From 307aa8265567b94e0610b7690b58c6b01988beab Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Mon, 19 Aug 2024 09:55:24 -0400
Subject: [PATCH 07/25] Updated container registry handling

---
 modules/local/arborview.nf          | 3 ++-
 modules/local/gas/mcluster/main.nf  | 2 +-
 modules/local/locidex/merge/main.nf | 5 +++--
 modules/local/profile_dists/main.nf | 3 ++-
 nextflow.config                     | 3 +++
 5 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/modules/local/arborview.nf b/modules/local/arborview.nf
index 787d8af..5b74e12 100644
--- a/modules/local/arborview.nf
+++ b/modules/local/arborview.nf
@@ -10,7 +10,8 @@ process ARBOR_VIEW {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     "docker.io/python:3.11.6" :
-    "docker.io/python:3.11.6" }"
+    task.ext.override_configured_container_registry != false ? 'docker.io/python:3.11.6' :
+    'python:3.11.6' }"
 
     input:
     tuple path(tree), path(contextual_data)
diff --git a/modules/local/gas/mcluster/main.nf b/modules/local/gas/mcluster/main.nf
index 0ba2761..7d832bb 100644
--- a/modules/local/gas/mcluster/main.nf
+++ b/modules/local/gas/mcluster/main.nf
@@ -6,7 +6,7 @@ process GAS_MCLUSTER{
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/genomic_address_service%3A0.1.1--pyh7cba7a3_1' :
-        'quay.io/biocontainers/genomic_address_service:0.1.1--pyh7cba7a3_1' }"
+        'biocontainers/genomic_address_service:0.1.1--pyh7cba7a3_1' }"
 
     input:
     path(dist_matrix)
diff --git a/modules/local/locidex/merge/main.nf b/modules/local/locidex/merge/main.nf
index 66ba9a7..d8ebb95 100644
--- a/modules/local/locidex/merge/main.nf
+++ b/modules/local/locidex/merge/main.nf
@@ -5,8 +5,9 @@ process LOCIDEX_MERGE {
     label 'process_medium'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    'docker.io/mwells14/locidex:0.2.2' :
-    'docker.io/mwells14/locidex:0.2.2' }"
+    "docker.io/mwells14/locidex:0.2.2" :
+    task.ext.override_configured_container_registry != false ? 'docker.io/mwells14/locidex:0.2.2' :
+    'mwells14/locidex:0.2.2' }"
 
     input:
     path input_values // [file(sample1), file(sample2), file(sample3), etc...]
diff --git a/modules/local/profile_dists/main.nf b/modules/local/profile_dists/main.nf
index 734d38d..24b3472 100644
--- a/modules/local/profile_dists/main.nf
+++ b/modules/local/profile_dists/main.nf
@@ -4,7 +4,8 @@ process PROFILE_DISTS{
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'docker.io/mwells14/gsp:arborator_1.0.0' :
-        'docker.io/mwells14/gsp:arborator_1.0.0' }"
+        task.ext.override_configured_container_registry != false ? 'docker.io/mwells14/gsp:arborator_1.0.0' :
+        'mwells14/gsp:arborator_1.0.0' }"
 
     input:
     path query
diff --git a/nextflow.config b/nextflow.config
index 1dad6fb..fbd25f5 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -178,6 +178,9 @@ docker.registry      = 'quay.io'
 podman.registry      = 'quay.io'
 singularity.registry = 'quay.io'
 
+// Override the default Docker registry when required
+process.ext.override_configured_container_registry = true
+
 // Nextflow plugins
 plugins {
     id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet

From 29d427fa7a2076e3119af7b29badcd110c993f18 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Mon, 19 Aug 2024 11:39:41 -0400
Subject: [PATCH 08/25] add user UID/GID to Nextflow Docker run in CI to fix
 getpwuid() error

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5abe80d..22bf0ad 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -56,4 +56,4 @@ jobs:
 
       - name: Nextflow run with test profile
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -with-docker -user $(id -u):$(id -g)

From 09cfa2b3cb461c583498bccc13de0a10a457647d Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Mon, 19 Aug 2024 12:27:27 -0400
Subject: [PATCH 09/25] add root user to Nextflow Docker run in CI to fix
 getpwuid() error

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 22bf0ad..6887f88 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -56,4 +56,4 @@ jobs:
 
       - name: Nextflow run with test profile
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -with-docker -user $(id -u):$(id -g)
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -with-docker -user root

From 2639645f103624bdfec1b9871bfaf9a15bf7ff1c Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Mon, 19 Aug 2024 13:26:03 -0400
Subject: [PATCH 10/25] Updated container for arborview

---
 modules/local/arborview.nf | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/modules/local/arborview.nf b/modules/local/arborview.nf
index 5b74e12..407468a 100644
--- a/modules/local/arborview.nf
+++ b/modules/local/arborview.nf
@@ -9,9 +9,8 @@ process ARBOR_VIEW {
     stageInMode 'copy' // Need to copy in arbor view html
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    "docker.io/python:3.11.6" :
-    task.ext.override_configured_container_registry != false ? 'docker.io/python:3.11.6' :
-    'python:3.11.6' }"
+    'https://depot.galaxyproject.org/singularity/python%3A3.12' :
+    'biocontainers/python:3.12' }"
 
     input:
     tuple path(tree), path(contextual_data)

From 726d2c968859cd87dfa3c697292821798972ccc0 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Mon, 19 Aug 2024 13:41:41 -0400
Subject: [PATCH 11/25] Refactor user configuration for locidex module: Remove
 --user specs from ci.yml and add to modules.conf

---
 .github/workflows/ci.yml | 2 +-
 conf/modules.config      | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6887f88..5abe80d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -56,4 +56,4 @@ jobs:
 
       - name: Nextflow run with test profile
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -with-docker -user root
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
diff --git a/conf/modules.config b/conf/modules.config
index 9e7bba6..046e121 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -48,6 +48,7 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null :
             filename.contains(File.separator) ? task.merged_prefix + filename.split(File.separator)[-1] : task.merged_prefix + filename }
         ]
+        containerOptions = '--user $(id -u):$(id -g)'
     }
 
     withName: PROFILE_DISTS {

From 8a016b40a008b00053aa9facde782565fd4f86a1 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Mon, 19 Aug 2024 14:01:03 -0400
Subject: [PATCH 12/25] Revert to previous user config in ci.yml

---
 .github/workflows/ci.yml | 2 +-
 conf/modules.config      | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5abe80d..fa95efb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -56,4 +56,4 @@ jobs:
 
       - name: Nextflow run with test profile
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -with-docker --user $(id -u):$(id -g)
diff --git a/conf/modules.config b/conf/modules.config
index 046e121..9e7bba6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -48,7 +48,6 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null :
             filename.contains(File.separator) ? task.merged_prefix + filename.split(File.separator)[-1] : task.merged_prefix + filename }
         ]
-        containerOptions = '--user $(id -u):$(id -g)'
     }
 
     withName: PROFILE_DISTS {

From eac46d87a1b7071f9e3884121546c39af3ca8a3b Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Mon, 19 Aug 2024 14:09:12 -0400
Subject: [PATCH 13/25] Update --user in ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fa95efb..6ba1c50 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -56,4 +56,4 @@ jobs:
 
       - name: Nextflow run with test profile
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -with-docker --user $(id -u):$(id -g)
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -with-docker --user 1001

From db503bf0ed1facc10c4432e753b4624b3f4eb46f Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Mon, 19 Aug 2024 15:42:13 -0400
Subject: [PATCH 14/25] Removed --user configurations for locidex

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6ba1c50..5abe80d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -56,4 +56,4 @@ jobs:
 
       - name: Nextflow run with test profile
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results -with-docker --user 1001
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

From 1aebb70540eafbb86be70f215bcb9de1b8af7ae3 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Tue, 20 Aug 2024 09:53:06 -0400
Subject: [PATCH 15/25] Updated CHANGELOG.md

---
 CHANGELOG.md | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0e5741b..45ccf8f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,15 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased] - 2024-08-20
+
+### Changed
+
+- Upgraded `locidex/merge` to version `0.2.2` and updated `input_assure` and test data for compatibility with the new `mlst.json` allele file format.
+  - [PR28](https://github.com/phac-nml/gasclustering/pull/28)
+- Aligned container registry handling in configuration files and modules with `phac-nml/pipeline-standards`
+  - [PR28](https://github.com/phac-nml/gasclustering/pull/28)
+
 ## [0.2.0] - 2024-06-26
 
 ### Added

From f3f83cd89320fbacdb0c856bb784668883ed4dfb Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Tue, 20 Aug 2024 14:35:11 -0400
Subject: [PATCH 16/25] Updated  release version

---
 CHANGELOG.md    | 2 +-
 nextflow.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 45ccf8f..1e39b34 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased] - 2024-08-20
+## [0.3.0] - 2024-08-21
 
 ### Changed
 
diff --git a/nextflow.config b/nextflow.config
index fbd25f5..a98e2dd 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -229,7 +229,7 @@ manifest {
     description     = """IRIDA Next Genomic Address Service Clustering Pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.2.0'
+    version         = '0.3.0'
     doi             = ''
     defaultBranch   = 'main'
 }

From a23379c8b18557814b2bf69bbf8232e4df57d4b1 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Tue, 20 Aug 2024 14:52:41 -0400
Subject: [PATCH 17/25] Removed print debugging statement in input_assure.py

---
 bin/input_assure.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/bin/input_assure.py b/bin/input_assure.py
index 7f5d56e..d4c2a1a 100755
--- a/bin/input_assure.py
+++ b/bin/input_assure.py
@@ -19,8 +19,6 @@ def check_inputs(json_file, sample_id, address, output_error_file, output_json_f
     with open_file(json_file, "rt") as f:
         json_data = json.load(f)
 
-    print(json.dumps(json_data, indent=4))
-
     # Extract the profile from the json_data
     profile = json_data.get("data", {}).get("profile", {})
     # Check for multiple keys in the JSON file and define error message

From 6f7f59d09714667e004dc55a70f6f7052ec5c7bd Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Tue, 20 Aug 2024 17:28:18 -0400
Subject: [PATCH 18/25] Replace unsorted list with sorted() for consistent
 ordering in input_assure.py

---
 bin/input_assure.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/input_assure.py b/bin/input_assure.py
index d4c2a1a..e2b7ac1 100755
--- a/bin/input_assure.py
+++ b/bin/input_assure.py
@@ -22,7 +22,7 @@ def check_inputs(json_file, sample_id, address, output_error_file, output_json_f
     # Extract the profile from the json_data
     profile = json_data.get("data", {}).get("profile", {})
     # Check for multiple keys in the JSON file and define error message
-    keys = list(profile.keys())
+    keys = sorted(profile.keys())
     original_key = keys[0] if keys else None
 
     # Define a variable to store the match_status (True or False)

From f787028216a2b1bbb8f15b32ea8d89c51399da20 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Wed, 21 Aug 2024 11:55:57 -0400
Subject: [PATCH 19/25] Update locidex to version 0.2.3

---
 modules/local/locidex/merge/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/locidex/merge/main.nf b/modules/local/locidex/merge/main.nf
index d8ebb95..103c24f 100644
--- a/modules/local/locidex/merge/main.nf
+++ b/modules/local/locidex/merge/main.nf
@@ -5,9 +5,9 @@ process LOCIDEX_MERGE {
     label 'process_medium'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    "docker.io/mwells14/locidex:0.2.2" :
-    task.ext.override_configured_container_registry != false ? 'docker.io/mwells14/locidex:0.2.2' :
-    'mwells14/locidex:0.2.2' }"
+    "docker.io/mwells14/locidex:0.2.3" :
+    task.ext.override_configured_container_registry != false ? 'docker.io/mwells14/locidex:0.2.3' :
+    'mwells14/locidex:0.2.3' }"
 
     input:
     path input_values // [file(sample1), file(sample2), file(sample3), etc...]

From cf5248e00d7514936f2e1e0f96750577200c6c26 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Wed, 21 Aug 2024 16:50:51 -0400
Subject: [PATCH 20/25] Add link to release tag

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1e39b34..79ef4ee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,3 +37,4 @@ Initial release of the Genomic Address Service Clustering pipeline to be used fo
 
 [0.1.0]: https://github.com/phac-nml/gasclustering/releases/tag/0.1.0
 [0.2.0]: https://github.com/phac-nml/gasclustering/releases/tag/0.2.0
+[0.3.0]: https://github.com/phac-nml/gasclustering/releases/tag/0.3.0

From e653503ef3f8cde25bdd8ac2c54475687b951e97 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Thu, 5 Sep 2024 10:39:51 -0400
Subject: [PATCH 21/25] Update CHANGELOG

---
 CHANGELOG.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 79ef4ee..e8e400a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,15 +3,17 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.3.0] - 2024-08-21
+## [0.3.0] - 2024-09-05
 
 ### Changed
 
-- Upgraded `locidex/merge` to version `0.2.2` and updated `input_assure` and test data for compatibility with the new `mlst.json` allele file format.
+- Upgraded `locidex/merge` to version `0.2.3` and updated `input_assure` and test data for compatibility with the new `mlst.json` allele file format.
   - [PR28](https://github.com/phac-nml/gasclustering/pull/28)
 - Aligned container registry handling in configuration files and modules with `phac-nml/pipeline-standards`
   - [PR28](https://github.com/phac-nml/gasclustering/pull/28)
 
+This pipeline is now compatible only with output generated by [Locidex v0.2.3+](https://github.com/phac-nml/locidex) and [Mikrokondo v0.4.0+](https://github.com/phac-nml/mikrokondo/releases/tag/v0.4.0).
+
 ## [0.2.0] - 2024-06-26
 
 ### Added

From dc32ebb45927b917dbe5b5cddb3fcca0750a2077 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Thu, 5 Sep 2024 10:40:15 -0400
Subject: [PATCH 22/25] Update test data file paths in samplesheets

---
 tests/data/samplesheets/samplesheet-hamming.csv             | 6 +++---
 tests/data/samplesheets/samplesheet-hash-missing.csv        | 6 +++---
 tests/data/samplesheets/samplesheet-hash-more-missing.csv   | 6 +++---
 tests/data/samplesheets/samplesheet-little-metadata.csv     | 6 +++---
 tests/data/samplesheets/samplesheet-mismatched-ids.csv      | 6 +++---
 tests/data/samplesheets/samplesheet-no-metadata.csv         | 6 +++---
 .../samplesheets/samplesheet-partial-mismatched-ids.csv     | 6 +++---
 tests/data/samplesheets/samplesheet-tabs.csv                | 6 +++---
 tests/data/samplesheets/samplesheet1.csv                    | 6 +++---
 9 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/tests/data/samplesheets/samplesheet-hamming.csv b/tests/data/samplesheets/samplesheet-hamming.csv
index df78ac4..d18a69c 100644
--- a/tests/data/samplesheets/samplesheet-hamming.csv
+++ b/tests/data/samplesheets/samplesheet-hamming.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample1.mlst.subtyping.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample2.mlst.subtyping.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hamming/sample3.mlst.subtyping.json,,,,,,,,
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hamming/sample1.mlst.subtyping.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hamming/sample2.mlst.subtyping.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hamming/sample3.mlst.subtyping.json,,,,,,,,
diff --git a/tests/data/samplesheets/samplesheet-hash-missing.csv b/tests/data/samplesheets/samplesheet-hash-missing.csv
index 6ad5929..9355c3d 100644
--- a/tests/data/samplesheets/samplesheet-hash-missing.csv
+++ b/tests/data/samplesheets/samplesheet-hash-missing.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample3.mlst.subtyping.json,,,,,,,,
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hash-missing/sample3.mlst.subtyping.json,,,,,,,,
diff --git a/tests/data/samplesheets/samplesheet-hash-more-missing.csv b/tests/data/samplesheets/samplesheet-hash-more-missing.csv
index 37f051f..4ee53c9 100644
--- a/tests/data/samplesheets/samplesheet-hash-more-missing.csv
+++ b/tests/data/samplesheets/samplesheet-hash-more-missing.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/case-hash-missing/sample3-more-missing.mlst.subtyping.json,,,,,,,,
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hash-missing/sample1.mlst.subtyping.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hash-missing/sample2.mlst.subtyping.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/case-hash-missing/sample3-more-missing.mlst.subtyping.json,,,,,,,,
diff --git a/tests/data/samplesheets/samplesheet-little-metadata.csv b/tests/data/samplesheets/samplesheet-little-metadata.csv
index 052b4b3..3e721de 100644
--- a/tests/data/samplesheets/samplesheet-little-metadata.csv
+++ b/tests/data/samplesheets/samplesheet-little-metadata.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,,,,1.4,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,3.1,3.2,,,,,,3.8
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,,,,1.4,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,3.1,3.2,,,,,,3.8
diff --git a/tests/data/samplesheets/samplesheet-mismatched-ids.csv b/tests/data/samplesheets/samplesheet-mismatched-ids.csv
index 6df7315..632768d 100644
--- a/tests/data/samplesheets/samplesheet-mismatched-ids.csv
+++ b/tests/data/samplesheets/samplesheet-mismatched-ids.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sampleA,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
-sampleB,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
-sampleC,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
+sampleA,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
+sampleB,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
+sampleC,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
diff --git a/tests/data/samplesheets/samplesheet-no-metadata.csv b/tests/data/samplesheets/samplesheet-no-metadata.csv
index 5f4d2ca..9d67864 100644
--- a/tests/data/samplesheets/samplesheet-no-metadata.csv
+++ b/tests/data/samplesheets/samplesheet-no-metadata.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,,,,,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,,,,,,,,
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,,,,,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,,,,,,,,
diff --git a/tests/data/samplesheets/samplesheet-partial-mismatched-ids.csv b/tests/data/samplesheets/samplesheet-partial-mismatched-ids.csv
index cd0655d..d5d42f0 100644
--- a/tests/data/samplesheets/samplesheet-partial-mismatched-ids.csv
+++ b/tests/data/samplesheets/samplesheet-partial-mismatched-ids.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sampleA,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
-sampleB,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
+sampleA,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
+sampleB,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
diff --git a/tests/data/samplesheets/samplesheet-tabs.csv b/tests/data/samplesheets/samplesheet-tabs.csv
index 4408655..56b4243 100644
--- a/tests/data/samplesheets/samplesheet-tabs.csv
+++ b/tests/data/samplesheets/samplesheet-tabs.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,a	b,,,,,,,
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,,,,a	b,,,,
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,,,,,,,,a	b
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,a	b,,,,,,,
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,,,,a	b,,,,
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,,,,,,,,a	b
diff --git a/tests/data/samplesheets/samplesheet1.csv b/tests/data/samplesheets/samplesheet1.csv
index f78cff3..3200344 100644
--- a/tests/data/samplesheets/samplesheet1.csv
+++ b/tests/data/samplesheets/samplesheet1.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8

From b60e1d3bfbf62cab71191defc64b851db9058e0e Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Thu, 5 Sep 2024 12:47:58 -0400
Subject: [PATCH 23/25] update assest/samplesheet.csv file paths

---
 assets/samplesheet.csv | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index b283ed7..82842ce 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,4 +1,4 @@
 sample,mlst_alleles
-sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample1.mlst.json
-sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample2.mlst.json
-sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/update/input_assure/tests/data/reports/sample3.mlst.json
+sample1,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample1.mlst.json
+sample2,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample2.mlst.json
+sample3,https://raw.githubusercontent.com/phac-nml/gasclustering/dev/tests/data/reports/sample3.mlst.json

From 0071ab8dacf22bb36fa0022fdcf84356d20f9866 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Tue, 10 Sep 2024 11:46:53 -0400
Subject: [PATCH 24/25] Update profile_dist container

---
 modules/local/profile_dists/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/profile_dists/main.nf b/modules/local/profile_dists/main.nf
index 24b3472..d316e78 100644
--- a/modules/local/profile_dists/main.nf
+++ b/modules/local/profile_dists/main.nf
@@ -3,9 +3,9 @@ process PROFILE_DISTS{
     tag "Pairwise Distance Generation"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker.io/mwells14/gsp:arborator_1.0.0' :
-        task.ext.override_configured_container_registry != false ? 'docker.io/mwells14/gsp:arborator_1.0.0' :
-        'mwells14/gsp:arborator_1.0.0' }"
+        'docker.io/mwells14/profile_dists:1.0.2' :
+        task.ext.override_configured_container_registry != false ? 'docker.io/mwells14/profile_dists:1.0.2' :
+        'mwells14/profile_dists:1.0.2' }"
 
     input:
     path query

From 0c358620a2283334247a03189c20fd1dd5b3e36a Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Tue, 10 Sep 2024 11:50:42 -0400
Subject: [PATCH 25/25] Update CHANGELOG

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e8e400a..9ad7753 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,10 +3,11 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.3.0] - 2024-09-05
+## [0.3.0] - 2024-09-10
 
 ### Changed
 
+- Upgraded `profile_dist` container to version `1.0.2`
 - Upgraded `locidex/merge` to version `0.2.3` and updated `input_assure` and test data for compatibility with the new `mlst.json` allele file format.
   - [PR28](https://github.com/phac-nml/gasclustering/pull/28)
 - Aligned container registry handling in configuration files and modules with `phac-nml/pipeline-standards`