diff --git a/src/main/python/trec-covid/covid_baseline_tools.py b/src/main/python/trec-covid/covid_baseline_tools.py
index aa18f3c08f..013044b122 100644
--- a/src/main/python/trec-covid/covid_baseline_tools.py
+++ b/src/main/python/trec-covid/covid_baseline_tools.py
@@ -13,7 +13,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-
+import math
 import os
 import re
 import subprocess
@@ -22,11 +22,11 @@
 
 
 def perform_runs(round_number, indexes):
-    base_topics = f'src/main/resources/topics-and-qrels/topics.covid-round{round_number}.xml'
-    udel_topics = f'src/main/resources/topics-and-qrels/topics.covid-round{round_number}-udel.xml'
+    base_topics = f'tools/topics-and-qrels/topics.covid-round{round_number}.xml'
+    udel_topics = f'tools/topics-and-qrels/topics.covid-round{round_number}-udel.xml'
 
     # Use cumulative qrels from previous round for relevance feedback runs
-    cumulative_qrels = f'src/main/resources/topics-and-qrels/qrels.covid-round{round_number - 1}-cumulative.txt'
+    cumulative_qrels = f'tools/topics-and-qrels/qrels.covid-round{round_number - 1}-cumulative.txt'
 
     print('')
     print('## Running on abstract index...')
@@ -119,7 +119,7 @@ def perform_fusion(round_number, run_checksums, check_md5=True):
 
 def prepare_final_submissions(round_number, run_checksums, check_md5=True):
     # Remove the cumulative qrels from the previous round.
-    qrels = f'src/main/resources/topics-and-qrels/qrels.covid-round{round_number - 1}-cumulative.txt'
+    qrels = f'tools/topics-and-qrels/qrels.covid-round{round_number - 1}-cumulative.txt'
 
     print('')
     print('## Preparing final submission files by removing qrels...')
@@ -235,8 +235,8 @@ def evaluate_runs(qrels, runs, expected={}, check_md5=True):
             for key in ['topics', 'ndcg_cut_10', 'judged_cut_10', 'ndcg_cut_20',
                         'judged_cut_20', 'map', 'recall_1000', 'judged_cut_1000']:
                 if key in expected[run]:
-                    assert metrics[key] == expected[run][key],\
-                        f'\'{key}\' doesn\'t match, expected {expected[run][key]} got {metrics[key]}!'
+                    assert math.isclose(metrics[key], expected[run][key], rel_tol=1e-4), \
+                        f'\'{key}\' doesn\'t match, expected {expected[run][key]:.4f} got {metrics[key]:.4f}!'
 
         if check_md5:
             assert metrics['md5'] == runs[run], f'Error in producing {run}!'
diff --git a/src/main/python/trec-covid/generate_query_udel.py b/src/main/python/trec-covid/generate_query_udel.py
index 4aa89c50d7..1120f34844 100755
--- a/src/main/python/trec-covid/generate_query_udel.py
+++ b/src/main/python/trec-covid/generate_query_udel.py
@@ -95,14 +95,14 @@
     original_query_file_name = f'topics.covid-round{args.round}.xml'
     original_query_file = os.path.join(
         args.anserini_root,
-        'src/main/resources/topics-and-qrels',
+        'tools/topics-and-qrels',
         original_query_file_name
     )
 
     output_query_file_name = f'topics.covid-round{args.round}-udel.xml'
     output_query_file = os.path.join(
         args.anserini_root,
-        'src/main/resources/topics-and-qrels',
+        'tools/topics-and-qrels',
         output_query_file_name
     )
 
diff --git a/src/main/python/trec-covid/generate_round1_baselines.py b/src/main/python/trec-covid/generate_round1_baselines.py
index a916cb6667..cfe89bedf9 100644
--- a/src/main/python/trec-covid/generate_round1_baselines.py
+++ b/src/main/python/trec-covid/generate_round1_baselines.py
@@ -54,8 +54,8 @@
 
 
 def perform_runs():
-    base_topics = f'src/main/resources/topics-and-qrels/topics.covid-round1.xml'
-    udel_topics = f'src/main/resources/topics-and-qrels/topics.covid-round1-udel.xml'
+    base_topics = f'tools/topics-and-qrels/topics.covid-round1.xml'
+    udel_topics = f'tools/topics-and-qrels/topics.covid-round1-udel.xml'
 
     print('')
     print('## Running on abstract index...')
@@ -178,7 +178,7 @@ def main():
     if not (os.path.isdir(indexes[0]) and os.path.isdir(indexes[1]) and os.path.isdir(indexes[2])):
         print('Required indexes do not exist. Please download first.')
 
-    round1_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round1.txt'
+    round1_qrels = 'tools/topics-and-qrels/qrels.covid-round1.txt'
 
     # Note that this script was written after this issue was noted: https://github.com/castorini/anserini/issues/1669
     # Thus, no point in checking MD5.
@@ -189,7 +189,7 @@ def main():
 
     expected_metrics = {
         'anserini.covid-r1.abstract.query.bm25.txt':
-            {'ndcg_cut_10': 0.4100, 'judged_cut_10': 0.8267, 'recall_1000': 0.5279},
+            {'ndcg_cut_10': 0.4100, 'judged_cut_10': 0.8267, 'recall_1000': 0.5285},
         'anserini.covid-r1.abstract.question.bm25.txt':
             {'ndcg_cut_10': 0.5179, 'judged_cut_10': 0.9833, 'recall_1000': 0.6313},
         'anserini.covid-r1.abstract.query+question.bm25.txt':
@@ -213,9 +213,9 @@ def main():
         'anserini.covid-r1.full-text.query-covid19.bm25.txt':
             {'ndcg_cut_10': 0.2434, 'judged_cut_10': 0.5233, 'recall_1000': 0.5692},
         'anserini.covid-r1.paragraph.query.bm25.txt':
-            {'ndcg_cut_10': 0.4302, 'judged_cut_10': 0.8400, 'recall_1000': 0.4327},
+            {'ndcg_cut_10': 0.4303, 'judged_cut_10': 0.8400, 'recall_1000': 0.4324},
         'anserini.covid-r1.paragraph.question.bm25.txt':
-            {'ndcg_cut_10': 0.4410, 'judged_cut_10': 0.9167, 'recall_1000': 0.5111},
+            {'ndcg_cut_10': 0.4410, 'judged_cut_10': 0.9167, 'recall_1000': 0.5108},
         'anserini.covid-r1.paragraph.query+question.bm25.txt':
             {'ndcg_cut_10': 0.5450, 'judged_cut_10': 0.9733, 'recall_1000': 0.5743},
         'anserini.covid-r1.paragraph.query+question+narrative.bm25.txt':
@@ -223,7 +223,7 @@ def main():
         'anserini.covid-r1.paragraph.query-udel.bm25.txt':
             {'ndcg_cut_10': 0.5544, 'judged_cut_10': 0.9200, 'recall_1000': 0.5640},
         'anserini.covid-r1.paragraph.query-covid19.bm25.txt':
-            {'ndcg_cut_10': 0.3180, 'judged_cut_10': 0.5333, 'recall_1000': 0.3552},
+            {'ndcg_cut_10': 0.3180, 'judged_cut_10': 0.5300, 'recall_1000': 0.3552},
         'anserini.covid-r1.fusion1.txt':
             {'ndcg_cut_10': 0.5716, 'judged_cut_10': 0.9867, 'recall_1000': 0.8122},
         'anserini.covid-r1.fusion2.txt':
diff --git a/src/main/python/trec-covid/generate_round2_baselines.py b/src/main/python/trec-covid/generate_round2_baselines.py
index 15bdefd667..4321525a5a 100644
--- a/src/main/python/trec-covid/generate_round2_baselines.py
+++ b/src/main/python/trec-covid/generate_round2_baselines.py
@@ -50,8 +50,8 @@
 
 
 def perform_runs():
-    base_topics = f'src/main/resources/topics-and-qrels/topics.covid-round2.xml'
-    udel_topics = f'src/main/resources/topics-and-qrels/topics.covid-round2-udel.xml'
+    base_topics = f'tools/topics-and-qrels/topics.covid-round2.xml'
+    udel_topics = f'tools/topics-and-qrels/topics.covid-round2-udel.xml'
 
     print('')
     print('## Running on abstract index...')
@@ -135,7 +135,7 @@ def perform_fusion(run_checksums, check_md5=True):
 
 def prepare_final_submissions(run_checksums, check_md5=True):
     # Remove the cumulative qrels from the previous round.
-    qrels = f'src/main/resources/topics-and-qrels/qrels.covid-round1.txt'
+    qrels = f'tools/topics-and-qrels/qrels.covid-round1.txt'
 
     print('')
     print('## Preparing final submission files by removing qrels...')
@@ -170,8 +170,8 @@ def main():
     if not (os.path.isdir(indexes[0]) and os.path.isdir(indexes[1]) and os.path.isdir(indexes[2])):
         print('Required indexes do not exist. Please download first.')
 
-    round1_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round1.txt'
-    round2_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round2.txt'
+    round1_qrels = 'tools/topics-and-qrels/qrels.covid-round1.txt'
+    round2_qrels = 'tools/topics-and-qrels/qrels.covid-round2.txt'
 
     # Note that this script was written after this issue was noted: https://github.com/castorini/anserini/issues/1669
     # Thus, no point in checking MD5.
@@ -183,11 +183,11 @@ def main():
 
     expected_metrics = {
         'anserini.covid-r2.abstract.qq.bm25.txt':
-            {'topics': 35, 'ndcg_cut_10': 0.3522, 'judged_cut_10': 0.5371, 'ndcg_cut_20': 0.3171,
+            {'topics': 35, 'ndcg_cut_10': 0.3521, 'judged_cut_10': 0.5371, 'ndcg_cut_20': 0.3170,
              'judged_cut_20': 0.5100, 'map': 0.1752, 'recall_1000': 0.6601, 'judged_cut_1000': 0.1013},
         'anserini.covid-r2.abstract.qdel.bm25.txt':
             {'topics': 35, 'ndcg_cut_10': 0.3781, 'judged_cut_10': 0.5371, 'ndcg_cut_20': 0.3462,
-             'judged_cut_20': 0.4829, 'map': 0.1804, 'recall_1000': 0.6485, 'judged_cut_1000': 0.0958},
+             'judged_cut_20': 0.4829, 'map': 0.1803, 'recall_1000': 0.6485, 'judged_cut_1000': 0.0958},
         'anserini.covid-r2.full-text.qq.bm25.txt':
             {'topics': 35, 'ndcg_cut_10': 0.2070, 'judged_cut_10': 0.4286, 'ndcg_cut_20': 0.1931,
              'judged_cut_20': 0.3929, 'map': 0.1159, 'recall_1000': 0.5953, 'judged_cut_1000': 0.0995},
@@ -195,11 +195,11 @@ def main():
             {'topics': 35, 'ndcg_cut_10': 0.3123, 'judged_cut_10': 0.4229, 'ndcg_cut_20': 0.2738,
              'judged_cut_20': 0.3929, 'map': 0.1473, 'recall_1000': 0.6517, 'judged_cut_1000': 0.1022},
         'anserini.covid-r2.paragraph.qq.bm25.txt':
-            {'topics': 35, 'ndcg_cut_10': 0.2772, 'judged_cut_10': 0.4400, 'ndcg_cut_20': 0.2579,
+            {'topics': 35, 'ndcg_cut_10': 0.2770, 'judged_cut_10': 0.4400, 'ndcg_cut_20': 0.2578,
              'judged_cut_20': 0.4529, 'map': 0.1607, 'recall_1000': 0.7248, 'judged_cut_1000': 0.1220},
         'anserini.covid-r2.paragraph.qdel.bm25.txt':
-            {'topics': 35, 'ndcg_cut_10': 0.3353, 'judged_cut_10': 0.4343, 'ndcg_cut_20': 0.2956,
-             'judged_cut_20': 0.4329, 'map': 0.1772, 'recall_1000': 0.7196, 'judged_cut_1000': 0.1136},
+            {'topics': 35, 'ndcg_cut_10': 0.3350, 'judged_cut_10': 0.4343, 'ndcg_cut_20': 0.2954,
+             'judged_cut_20': 0.4329, 'map': 0.1772, 'recall_1000': 0.7196, 'judged_cut_1000': 0.1137},
         'anserini.covid-r2.fusion1.txt':
             {'topics': 35, 'ndcg_cut_10': 0.3297, 'judged_cut_10': 0.4657, 'ndcg_cut_20': 0.3060,
              'judged_cut_20': 0.4643, 'map': 0.1914, 'recall_1000': 0.7561, 'judged_cut_1000': 0.1304},
@@ -216,7 +216,7 @@ def main():
             {'topics': 35, 'ndcg_cut_10': 0.4827, 'judged_cut_10': 0.9543, 'ndcg_cut_20': 0.4512,
              'judged_cut_20': 0.8614, 'map': 0.2431, 'recall_1000': 0.6475, 'judged_cut_1000': 0.1463},
         'anserini.final-r2.fusion2.txt':
-            {'topics': 35, 'ndcg_cut_10': 0.5553, 'judged_cut_10': 0.9743, 'ndcg_cut_20': 0.5058,
+            {'topics': 35, 'ndcg_cut_10': 0.5553, 'judged_cut_10': 0.9714, 'ndcg_cut_20': 0.5058,
              'judged_cut_20': 0.8957, 'map': 0.2739, 'recall_1000': 0.6832, 'judged_cut_1000': 0.1528},
     }
     evaluate_runs(round2_qrels, final_runs, expected=expected_metrics, check_md5=check_md5_flag)
diff --git a/src/main/python/trec-covid/generate_round3_baselines.py b/src/main/python/trec-covid/generate_round3_baselines.py
index 40032370ca..9310ec3bed 100644
--- a/src/main/python/trec-covid/generate_round3_baselines.py
+++ b/src/main/python/trec-covid/generate_round3_baselines.py
@@ -89,13 +89,13 @@ def main():
     if not (os.path.isdir(indexes[0]) and os.path.isdir(indexes[1]) and os.path.isdir(indexes[2])):
         print('Required indexes do not exist. Please download first.')
 
-    os.system('cat src/main/resources/topics-and-qrels/qrels.covid-round1.txt ' +
-              'src/main/resources/topics-and-qrels/qrels.covid-round2.txt ' +
-              '> src/main/resources/topics-and-qrels/qrels.covid-round2-cumulative.txt')
+    os.system('cat tools/topics-and-qrels/qrels.covid-round1.txt ' +
+              'tools/topics-and-qrels/qrels.covid-round2.txt ' +
+              '> tools/topics-and-qrels/qrels.covid-round2-cumulative.txt')
 
-    round2_cumulative_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round2-cumulative.txt'
-    round3_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round3.txt'
-    round3_cumulative_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round3-cumulative.txt'
+    round2_cumulative_qrels = 'tools/topics-and-qrels/qrels.covid-round2-cumulative.txt'
+    round3_qrels = 'tools/topics-and-qrels/qrels.covid-round3.txt'
+    round3_cumulative_qrels = 'tools/topics-and-qrels/qrels.covid-round3-cumulative.txt'
 
     # MD5 checksums don't match anymore, see https://github.com/castorini/anserini/issues/1669
     check_md5_flag = False
@@ -107,11 +107,11 @@ def main():
 
     expected_metrics = {
         'anserini.covid-r3.abstract.qq.bm25.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.2117, 'judged_cut_10': 0.3300, 'ndcg_cut_20': 0.2043,
-             'judged_cut_20': 0.3150, 'map': 0.0951, 'recall_1000': 0.4398, 'judged_cut_1000': 0.1275},
+            {'topics': 40, 'ndcg_cut_10': 0.2136, 'judged_cut_10': 0.3275, 'ndcg_cut_20': 0.2040,
+             'judged_cut_20': 0.3138, 'map': 0.0950, 'recall_1000': 0.4398, 'judged_cut_1000': 0.1275},
         'anserini.covid-r3.abstract.qdel.bm25.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.2466, 'judged_cut_10': 0.3375, 'ndcg_cut_20': 0.2253,
-             'judged_cut_20': 0.3175, 'map': 0.1023, 'recall_1000': 0.4537, 'judged_cut_1000': 0.1248},
+            {'topics': 40, 'ndcg_cut_10': 0.2478, 'judged_cut_10': 0.3325, 'ndcg_cut_20': 0.2283,
+             'judged_cut_20': 0.3175, 'map': 0.1025, 'recall_1000': 0.4537, 'judged_cut_1000': 0.1249},
         'anserini.covid-r3.full-text.qq.bm25.txt':
             {'topics': 40, 'ndcg_cut_10': 0.2337, 'judged_cut_10': 0.4650, 'ndcg_cut_20': 0.2259,
              'judged_cut_20': 0.4425, 'map': 0.1099, 'recall_1000': 0.4817, 'judged_cut_1000': 0.1490},
@@ -119,30 +119,30 @@ def main():
             {'topics': 40, 'ndcg_cut_10': 0.3430, 'judged_cut_10': 0.5025, 'ndcg_cut_20': 0.3077,
              'judged_cut_20': 0.4888, 'map': 0.1426, 'recall_1000': 0.5267, 'judged_cut_1000': 0.1575},
         'anserini.covid-r3.paragraph.qq.bm25.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.2848, 'judged_cut_10': 0.5175, 'ndcg_cut_20': 0.2734,
-             'judged_cut_20': 0.4938, 'map': 0.1390, 'recall_1000': 0.5527, 'judged_cut_1000': 0.1727},
+            {'topics': 40, 'ndcg_cut_10': 0.2843, 'judged_cut_10': 0.5175, 'ndcg_cut_20': 0.2731,
+             'judged_cut_20': 0.4938, 'map': 0.1389, 'recall_1000': 0.5527, 'judged_cut_1000': 0.1727},
         'anserini.covid-r3.paragraph.qdel.bm25.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.3604, 'judged_cut_10': 0.5050, 'ndcg_cut_20': 0.3213,
-             'judged_cut_20': 0.4875, 'map': 0.1520, 'recall_1000': 0.5676, 'judged_cut_1000': 0.1672},
+            {'topics': 40, 'ndcg_cut_10': 0.3598, 'judged_cut_10': 0.5050, 'ndcg_cut_20': 0.3209,
+             'judged_cut_20': 0.4875, 'map': 0.1519, 'recall_1000': 0.5676, 'judged_cut_1000': 0.1672},
         'anserini.covid-r3.fusion1.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.3093, 'judged_cut_10': 0.4975, 'ndcg_cut_20': 0.2933,
-             'judged_cut_20': 0.5025, 'map': 0.1400, 'recall_1000': 0.5566, 'judged_cut_1000': 0.1750},
+            {'topics': 40, 'ndcg_cut_10': 0.3065, 'judged_cut_10': 0.4950, 'ndcg_cut_20': 0.2923,
+             'judged_cut_20': 0.5012, 'map': 0.1399, 'recall_1000': 0.5566, 'judged_cut_1000': 0.1750},
         'anserini.covid-r3.fusion2.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.3568, 'judged_cut_10': 0.5250, 'ndcg_cut_20': 0.3273,
-             'judged_cut_20': 0.4925, 'map': 0.1564, 'recall_1000': 0.5769, 'judged_cut_1000': 0.1715},
+            {'topics': 40, 'ndcg_cut_10': 0.3559, 'judged_cut_10': 0.5250, 'ndcg_cut_20': 0.3263,
+             'judged_cut_20': 0.4925, 'map': 0.1563, 'recall_1000': 0.5769, 'judged_cut_1000': 0.1715},
         'anserini.covid-r3.abstract.qdel.bm25+rm3Rf.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.3633, 'judged_cut_10': 0.3800, 'ndcg_cut_20': 0.3175,
-             'judged_cut_20': 0.3600, 'map': 0.1526, 'recall_1000': 0.5722, 'judged_cut_1000': 0.1398},
+            {'topics': 40, 'ndcg_cut_10': 0.3616, 'judged_cut_10': 0.3775, 'ndcg_cut_20': 0.3174,
+             'judged_cut_20': 0.3575, 'map': 0.1525, 'recall_1000': 0.5715, 'judged_cut_1000': 0.1398},
     }
     evaluate_runs(round2_cumulative_qrels, cumulative_runs, expected=expected_metrics, check_md5=check_md5_flag)
 
     expected_metrics = {
         'anserini.covid-r3.abstract.qq.bm25.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.5780, 'judged_cut_10': 0.8875, 'ndcg_cut_20': 0.5359,
-             'judged_cut_20': 0.8325, 'map': 0.2348, 'recall_1000': 0.5040, 'judged_cut_1000': 0.2351},
+            {'topics': 40, 'ndcg_cut_10': 0.5804, 'judged_cut_10': 0.8875, 'ndcg_cut_20': 0.5377,
+             'judged_cut_20': 0.8325, 'map': 0.2347, 'recall_1000': 0.5039, 'judged_cut_1000': 0.2351},
         'anserini.covid-r3.abstract.qdel.bm25.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.6289, 'judged_cut_10': 0.9300, 'ndcg_cut_20': 0.5971,
-             'judged_cut_20': 0.8925, 'map': 0.2525, 'recall_1000': 0.5215, 'judged_cut_1000': 0.2370},
+            {'topics': 40, 'ndcg_cut_10': 0.6295, 'judged_cut_10': 0.9275, 'ndcg_cut_20': 0.5989,
+             'judged_cut_20': 0.8912, 'map': 0.2524, 'recall_1000': 0.5214, 'judged_cut_1000': 0.2370},
         'anserini.covid-r3.full-text.qq.bm25.txt':
             {'topics': 40, 'ndcg_cut_10': 0.3977, 'judged_cut_10': 0.7500, 'ndcg_cut_20': 0.3681,
              'judged_cut_20': 0.7213, 'map': 0.1646, 'recall_1000': 0.4708, 'judged_cut_1000': 0.2471},
@@ -150,39 +150,39 @@ def main():
             {'topics': 40, 'ndcg_cut_10': 0.5790, 'judged_cut_10': 0.9050, 'ndcg_cut_20': 0.5234,
              'judged_cut_20': 0.8525, 'map': 0.2236, 'recall_1000': 0.5313, 'judged_cut_1000': 0.2693},
         'anserini.covid-r3.paragraph.qq.bm25.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.5396, 'judged_cut_10': 0.9425, 'ndcg_cut_20': 0.5079,
+            {'topics': 40, 'ndcg_cut_10': 0.5397, 'judged_cut_10': 0.9425, 'ndcg_cut_20': 0.5079,
              'judged_cut_20': 0.9050, 'map': 0.2498, 'recall_1000': 0.5766, 'judged_cut_1000': 0.2978},
         'anserini.covid-r3.paragraph.qdel.bm25.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.6327, 'judged_cut_10': 0.9600, 'ndcg_cut_20': 0.5793,
+            {'topics': 40, 'ndcg_cut_10': 0.6328, 'judged_cut_10': 0.9600, 'ndcg_cut_20': 0.5793,
              'judged_cut_20': 0.9162, 'map': 0.2753, 'recall_1000': 0.5923, 'judged_cut_1000': 0.2956},
         'anserini.covid-r3.fusion1.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.5924, 'judged_cut_10': 0.9625, 'ndcg_cut_20': 0.5563,
+            {'topics': 40, 'ndcg_cut_10': 0.5917, 'judged_cut_10': 0.9625, 'ndcg_cut_20': 0.5559,
              'judged_cut_20': 0.9362, 'map': 0.2700, 'recall_1000': 0.5956, 'judged_cut_1000': 0.3045},
         'anserini.covid-r3.fusion2.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.6515, 'judged_cut_10': 0.9875, 'ndcg_cut_20': 0.6200,
-             'judged_cut_20': 0.9675, 'map': 0.3027, 'recall_1000': 0.6194, 'judged_cut_1000': 0.3076},
+            {'topics': 40, 'ndcg_cut_10': 0.6508, 'judged_cut_10': 0.9875, 'ndcg_cut_20': 0.6184,
+             'judged_cut_20': 0.9663, 'map': 0.3026, 'recall_1000': 0.6194, 'judged_cut_1000': 0.3076},
         'anserini.covid-r3.abstract.qdel.bm25+rm3Rf.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.7459, 'judged_cut_10': 0.9875, 'ndcg_cut_20': 0.7023,
-             'judged_cut_20': 0.9637, 'map': 0.3190, 'recall_1000': 0.6125, 'judged_cut_1000': 0.2600},
+            {'topics': 40, 'ndcg_cut_10': 0.7411, 'judged_cut_10': 0.9850, 'ndcg_cut_20': 0.7007,
+             'judged_cut_20': 0.9637, 'map': 0.3186, 'recall_1000': 0.6113, 'judged_cut_1000': 0.2598},
     }
     evaluate_runs(round3_cumulative_qrels, cumulative_runs, expected=expected_metrics, check_md5=check_md5_flag)
 
     expected_metrics = {
         'anserini.final-r3.fusion1.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.5339, 'judged_cut_10': 0.8400, 'ndcg_cut_20': 0.4875,
-             'judged_cut_20': 0.7637, 'map': 0.2283, 'recall_1000': 0.6160, 'judged_cut_1000': 0.1370},
+            {'topics': 40, 'ndcg_cut_10': 0.5337, 'judged_cut_10': 0.8400, 'ndcg_cut_20': 0.4874,
+             'judged_cut_20': 0.7637, 'map': 0.2284, 'recall_1000': 0.6158, 'judged_cut_1000': 0.1370},
         'anserini.final-r3.fusion1.post-processed.txt':
             {'topics': 40, 'ndcg_cut_10': 0.5359, 'judged_cut_10': 0.8475, 'ndcg_cut_20': 0.4902,
              'judged_cut_20': 0.7675, 'map': 0.2293, 'recall_1000': 0.6160, 'judged_cut_1000': 0.1373},
         'anserini.final-r3.fusion2.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.6072, 'judged_cut_10': 0.9025, 'ndcg_cut_20': 0.5599,
-             'judged_cut_20': 0.8337, 'map': 0.2631, 'recall_1000': 0.6441, 'judged_cut_1000': 0.1431},
+            {'topics': 40, 'ndcg_cut_10': 0.6058, 'judged_cut_10': 0.9025, 'ndcg_cut_20': 0.5596,
+             'judged_cut_20': 0.8350, 'map': 0.2631, 'recall_1000': 0.6441, 'judged_cut_1000': 0.1431},
         'anserini.final-r3.fusion2.post-processed.txt':
             {'topics': 40, 'ndcg_cut_10': 0.6100, 'judged_cut_10': 0.9100, 'ndcg_cut_20': 0.5617,
              'judged_cut_20': 0.8375, 'map': 0.2641, 'recall_1000': 0.6441, 'judged_cut_1000': 0.1434},
         'anserini.final-r3.rf.txt':
-            {'topics': 40, 'ndcg_cut_10': 0.6812, 'judged_cut_10': 0.9600, 'ndcg_cut_20': 0.6255,
-             'judged_cut_20': 0.8450, 'map': 0.2787, 'recall_1000': 0.6399, 'judged_cut_1000': 0.1246},
+            {'topics': 40, 'ndcg_cut_10': 0.6793, 'judged_cut_10': 0.9575, 'ndcg_cut_20': 0.6251,
+             'judged_cut_20': 0.8500, 'map': 0.2783, 'recall_1000': 0.6390, 'judged_cut_1000': 0.1247},
         'anserini.final-r3.rf.post-processed.txt':
             {'topics': 40, 'ndcg_cut_10': 0.6883, 'judged_cut_10': 0.9750, 'ndcg_cut_20': 0.6321,
              'judged_cut_20': 0.8538, 'map': 0.2817, 'recall_1000': 0.6399, 'judged_cut_1000': 0.1250},
diff --git a/src/main/python/trec-covid/generate_round4_baselines.py b/src/main/python/trec-covid/generate_round4_baselines.py
index 2c7c0562e8..c869d5d9d7 100644
--- a/src/main/python/trec-covid/generate_round4_baselines.py
+++ b/src/main/python/trec-covid/generate_round4_baselines.py
@@ -89,9 +89,9 @@ def main():
     if not (os.path.isdir(indexes[0]) and os.path.isdir(indexes[1]) and os.path.isdir(indexes[2])):
         print('Required indexes do not exist. Please download first.')
 
-    round3_cumulative_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round3-cumulative.txt'
-    round4_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round4.txt'
-    round4_cumulative_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round4-cumulative.txt'
+    round3_cumulative_qrels = 'tools/topics-and-qrels/qrels.covid-round3-cumulative.txt'
+    round4_qrels = 'tools/topics-and-qrels/qrels.covid-round4.txt'
+    round4_cumulative_qrels = 'tools/topics-and-qrels/qrels.covid-round4-cumulative.txt'
 
     # MD5 checksums don't match anymore, see https://github.com/castorini/anserini/issues/1669
     check_md5_flag = False
@@ -103,11 +103,11 @@ def main():
 
     expected_metrics = {
         'anserini.covid-r4.abstract.qq.bm25.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.3143, 'judged_cut_10': 0.4467, 'ndcg_cut_20': 0.2993,
-             'judged_cut_20': 0.4367, 'map': 0.1296, 'recall_1000': 0.4257, 'judged_cut_1000': 0.1672},
+            {'topics': 45, 'ndcg_cut_10': 0.3084, 'judged_cut_10': 0.4444, 'ndcg_cut_20': 0.2964,
+             'judged_cut_20': 0.4367, 'map': 0.1292, 'recall_1000': 0.4257, 'judged_cut_1000': 0.1671},
         'anserini.covid-r4.abstract.qdel.bm25.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.3260, 'judged_cut_10': 0.4378, 'ndcg_cut_20': 0.3188,
-             'judged_cut_20': 0.4511, 'map': 0.1383, 'recall_1000': 0.4432, 'judged_cut_1000': 0.1706},
+            {'topics': 45, 'ndcg_cut_10': 0.3230, 'judged_cut_10': 0.4378, 'ndcg_cut_20': 0.3159,
+             'judged_cut_20': 0.4489, 'map': 0.1381, 'recall_1000': 0.4433, 'judged_cut_1000': 0.1706},
         'anserini.covid-r4.full-text.qq.bm25.txt':
             {'topics': 45, 'ndcg_cut_10': 0.2108, 'judged_cut_10': 0.4044, 'ndcg_cut_20': 0.2119,
              'judged_cut_20': 0.4011, 'map': 0.1007, 'recall_1000': 0.3891, 'judged_cut_1000': 0.1776},
@@ -115,30 +115,30 @@ def main():
             {'topics': 45, 'ndcg_cut_10': 0.3499, 'judged_cut_10': 0.5067, 'ndcg_cut_20': 0.3260,
              'judged_cut_20': 0.4833, 'map': 0.1399, 'recall_1000': 0.4537, 'judged_cut_1000': 0.1952},
         'anserini.covid-r4.paragraph.qq.bm25.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.3229, 'judged_cut_10': 0.5267, 'ndcg_cut_20': 0.3072,
-             'judged_cut_20': 0.5022, 'map': 0.1481, 'recall_1000': 0.4863, 'judged_cut_1000': 0.2110},
+            {'topics': 45, 'ndcg_cut_10': 0.3228, 'judged_cut_10': 0.5267, 'ndcg_cut_20': 0.3072,
+             'judged_cut_20': 0.5022, 'map': 0.1480, 'recall_1000': 0.4863, 'judged_cut_1000': 0.2110},
         'anserini.covid-r4.paragraph.qdel.bm25.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.4016, 'judged_cut_10': 0.5333, 'ndcg_cut_20': 0.3666,
-             'judged_cut_20': 0.4978, 'map': 0.1647, 'recall_1000': 0.5050, 'judged_cut_1000': 0.2098},
+            {'topics': 45, 'ndcg_cut_10': 0.4011, 'judged_cut_10': 0.5333, 'ndcg_cut_20': 0.3663,
+             'judged_cut_20': 0.4978, 'map': 0.1647, 'recall_1000': 0.5050, 'judged_cut_1000': 0.2099},
         'anserini.covid-r4.fusion1.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.3424, 'judged_cut_10': 0.5289, 'ndcg_cut_20': 0.3345,
-             'judged_cut_20': 0.5278, 'map': 0.1495, 'recall_1000': 0.5033, 'judged_cut_1000': 0.2160},
+            {'topics': 45, 'ndcg_cut_10': 0.3446, 'judged_cut_10': 0.5289, 'ndcg_cut_20': 0.3358,
+             'judged_cut_20': 0.5289, 'map': 0.1496, 'recall_1000': 0.5033, 'judged_cut_1000': 0.2160},
         'anserini.covid-r4.fusion2.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.4004, 'judged_cut_10': 0.5400, 'ndcg_cut_20': 0.3743,
-             'judged_cut_20': 0.5111, 'map': 0.1713, 'recall_1000': 0.5291, 'judged_cut_1000': 0.2186},
+            {'topics': 45, 'ndcg_cut_10': 0.3987, 'judged_cut_10': 0.5378, 'ndcg_cut_20': 0.3743,
+             'judged_cut_20': 0.5100, 'map': 0.1712, 'recall_1000': 0.5291, 'judged_cut_1000': 0.2186},
         'anserini.covid-r4.abstract.qdel.bm25+rm3Rf.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.4598, 'judged_cut_10': 0.5044, 'ndcg_cut_20': 0.4404,
-             'judged_cut_20': 0.5167, 'map': 0.1909, 'recall_1000': 0.5330, 'judged_cut_1000': 0.1889},
+            {'topics': 45, 'ndcg_cut_10': 0.4521, 'judged_cut_10': 0.5000, 'ndcg_cut_20': 0.4388,
+             'judged_cut_20': 0.5167, 'map': 0.1904, 'recall_1000': 0.5322, 'judged_cut_1000': 0.1888},
     }
     evaluate_runs(round3_cumulative_qrels, cumulative_runs, expected=expected_metrics, check_md5=check_md5_flag)
 
     expected_metrics = {
         'anserini.covid-r4.abstract.qq.bm25.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.6600, 'judged_cut_10': 0.9356, 'ndcg_cut_20': 0.6120,
-             'judged_cut_20': 0.9111, 'map': 0.2780, 'recall_1000': 0.5019, 'judged_cut_1000': 0.2876},
+            {'topics': 45, 'ndcg_cut_10': 0.6619, 'judged_cut_10': 0.9356, 'ndcg_cut_20': 0.6147,
+             'judged_cut_20': 0.9100, 'map': 0.2779, 'recall_1000': 0.5018, 'judged_cut_1000': 0.2876},
         'anserini.covid-r4.abstract.qdel.bm25.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.7081, 'judged_cut_10': 0.9844, 'ndcg_cut_20': 0.6650,
-             'judged_cut_20': 0.9622, 'map': 0.2994, 'recall_1000': 0.5233, 'judged_cut_1000': 0.2987},
+            {'topics': 45, 'ndcg_cut_10': 0.7087, 'judged_cut_10': 0.9844, 'ndcg_cut_20': 0.6662,
+             'judged_cut_20': 0.9633, 'map': 0.2993, 'recall_1000': 0.5233, 'judged_cut_1000': 0.2987},
         'anserini.covid-r4.full-text.qq.bm25.txt':
             {'topics': 45, 'ndcg_cut_10': 0.4192, 'judged_cut_10': 0.8067, 'ndcg_cut_20': 0.3984,
              'judged_cut_20': 0.7544, 'map': 0.1712, 'recall_1000': 0.4139, 'judged_cut_1000': 0.2740},
@@ -149,36 +149,36 @@ def main():
             {'topics': 45, 'ndcg_cut_10': 0.5610, 'judged_cut_10': 0.9133, 'ndcg_cut_20': 0.5324,
              'judged_cut_20': 0.8756, 'map': 0.2713, 'recall_1000': 0.5385, 'judged_cut_1000': 0.3386},
         'anserini.covid-r4.paragraph.qdel.bm25.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.6477, 'judged_cut_10': 0.9644, 'ndcg_cut_20': 0.6084,
+            {'topics': 45, 'ndcg_cut_10': 0.6476, 'judged_cut_10': 0.9644, 'ndcg_cut_20': 0.6084,
              'judged_cut_20': 0.9322, 'map': 0.2975, 'recall_1000': 0.5625, 'judged_cut_1000': 0.3443},
         'anserini.covid-r4.fusion1.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.6271, 'judged_cut_10': 0.9689, 'ndcg_cut_20': 0.5968,
-             'judged_cut_20': 0.9422, 'map': 0.2904, 'recall_1000': 0.5623, 'judged_cut_1000': 0.3519},
+            {'topics': 45, 'ndcg_cut_10': 0.6279, 'judged_cut_10': 0.9689, 'ndcg_cut_20': 0.5969,
+             'judged_cut_20': 0.9422, 'map': 0.2904, 'recall_1000': 0.5623, 'judged_cut_1000': 0.3520},
         'anserini.covid-r4.fusion2.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.6802, 'judged_cut_10': 1.0000, 'ndcg_cut_20': 0.6573,
-             'judged_cut_20': 0.9956, 'map': 0.3286, 'recall_1000': 0.5946, 'judged_cut_1000': 0.3625},
+            {'topics': 45, 'ndcg_cut_10': 0.6803, 'judged_cut_10': 1.0000, 'ndcg_cut_20': 0.6577,
+             'judged_cut_20': 0.9956, 'map': 0.3286, 'recall_1000': 0.5947, 'judged_cut_1000': 0.3626},
         'anserini.covid-r4.abstract.qdel.bm25+rm3Rf.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.8056, 'judged_cut_10': 1.0000, 'ndcg_cut_20': 0.7649,
-             'judged_cut_20': 0.9967, 'map': 0.3663, 'recall_1000': 0.5955, 'judged_cut_1000': 0.3229},
+            {'topics': 45, 'ndcg_cut_10': 0.8057, 'judged_cut_10': 1.0000, 'ndcg_cut_20': 0.7661,
+             'judged_cut_20': 0.9978, 'map': 0.3661, 'recall_1000': 0.5951, 'judged_cut_1000': 0.3229},
     }
     evaluate_runs(round4_cumulative_qrels, cumulative_runs, expected=expected_metrics, check_md5=check_md5_flag)
 
     expected_metrics = {
         'anserini.final-r4.fusion1.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.5629, 'judged_cut_10': 0.8578, 'ndcg_cut_20': 0.5204,
-             'judged_cut_20': 0.7922, 'map': 0.2656, 'recall_1000': 0.6571, 'judged_cut_1000': 0.1474},
+            {'topics': 45, 'ndcg_cut_10': 0.5632, 'judged_cut_10': 0.8578, 'ndcg_cut_20': 0.5211,
+             'judged_cut_20': 0.7933, 'map': 0.2657, 'recall_1000': 0.6573, 'judged_cut_1000': 0.1474},
         'anserini.final-r4.fusion1.post-processed.txt':
             {'topics': 45, 'ndcg_cut_10': 0.5658, 'judged_cut_10': 0.8578, 'ndcg_cut_20': 0.5244,
              'judged_cut_20': 0.7978, 'map': 0.2666, 'recall_1000': 0.6571, 'judged_cut_1000': 0.1475},
         'anserini.final-r4.fusion2.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.6376, 'judged_cut_10': 0.9778, 'ndcg_cut_20': 0.6047,
-             'judged_cut_20': 0.8978, 'map': 0.3078, 'recall_1000': 0.6928, 'judged_cut_1000': 0.1558},
+            {'topics': 45, 'ndcg_cut_10': 0.6389, 'judged_cut_10': 0.9778, 'ndcg_cut_20': 0.6054,
+             'judged_cut_20': 0.8989, 'map': 0.3077, 'recall_1000': 0.6928, 'judged_cut_1000': 0.1559},
         'anserini.final-r4.fusion2.post-processed.txt':
             {'topics': 45, 'ndcg_cut_10': 0.6428, 'judged_cut_10': 0.9844, 'ndcg_cut_20': 0.6089,
              'judged_cut_20': 0.9022, 'map': 0.3088, 'recall_1000': 0.6928, 'judged_cut_1000': 0.1559},
         'anserini.final-r4.rf.txt':
-            {'topics': 45, 'ndcg_cut_10': 0.7472, 'judged_cut_10': 0.9778, 'ndcg_cut_20': 0.6940,
-             'judged_cut_20': 0.9233, 'map': 0.3506, 'recall_1000': 0.6962, 'judged_cut_1000': 0.1408},
+            {'topics': 45, 'ndcg_cut_10': 0.7471, 'judged_cut_10': 0.9756, 'ndcg_cut_20': 0.6960,
+             'judged_cut_20': 0.9244, 'map': 0.3504, 'recall_1000': 0.6960, 'judged_cut_1000': 0.1408},
         'anserini.final-r4.rf.post-processed.txt':
             {'topics': 45, 'ndcg_cut_10': 0.7516, 'judged_cut_10': 0.9867, 'ndcg_cut_20': 0.6976,
              'judged_cut_20': 0.9278, 'map': 0.3519, 'recall_1000': 0.6962, 'judged_cut_1000': 0.1409},
diff --git a/src/main/python/trec-covid/generate_round4_doc2query_baselines.py b/src/main/python/trec-covid/generate_round4_doc2query_baselines.py
index 21d67a9877..f80347d7e9 100644
--- a/src/main/python/trec-covid/generate_round4_doc2query_baselines.py
+++ b/src/main/python/trec-covid/generate_round4_doc2query_baselines.py
@@ -78,8 +78,8 @@
 
 
 def perform_runs(cumulative_qrels):
-    base_topics = 'src/main/resources/topics-and-qrels/topics.covid-round4.xml'
-    udel_topics = 'src/main/resources/topics-and-qrels/topics.covid-round4-udel.xml'
+    base_topics = 'tools/topics-and-qrels/topics.covid-round4.xml'
+    udel_topics = 'tools/topics-and-qrels/topics.covid-round4-udel.xml'
 
     print('')
     print('## Running on abstract index...')
@@ -213,9 +213,9 @@ def main():
     if not (os.path.isdir(indexes[0]) and os.path.isdir(indexes[1]) and os.path.isdir(indexes[2])):
         print('Required indexes do not exist. Please download first.')
 
-    round3_cumulative_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round3-cumulative.txt'
-    round4_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round4.txt'
-    round4_cumulative_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round4-cumulative.txt'
+    round3_cumulative_qrels = 'tools/topics-and-qrels/qrels.covid-round3-cumulative.txt'
+    round4_qrels = 'tools/topics-and-qrels/qrels.covid-round4.txt'
+    round4_cumulative_qrels = 'tools/topics-and-qrels/qrels.covid-round4-cumulative.txt'
 
     # MD5 checksums don't match anymore, see https://github.com/castorini/anserini/issues/1669
     check_md5_flag = False
@@ -259,7 +259,7 @@ def main():
     expected_metrics = {
         'expanded.anserini.final-r4.fusion1.txt':
             {'topics': 45, 'ndcg_cut_10': 0.5395, 'judged_cut_10': 0.7222, 'ndcg_cut_20': 0.5115,
-             'judged_cut_20': 0.6944, 'map': 0.2497, 'recall_1000': 0.6717, 'judged_cut_1000': 0.1424},
+             'judged_cut_20': 0.6944, 'map': 0.2498, 'recall_1000': 0.6717, 'judged_cut_1000': 0.1424},
         'expanded.anserini.final-r4.fusion2.txt':
             {'topics': 45, 'ndcg_cut_10': 0.5630, 'judged_cut_10': 0.7444, 'ndcg_cut_20': 0.5175,
              'judged_cut_20': 0.6911, 'map': 0.2550, 'recall_1000': 0.6800, 'judged_cut_1000': 0.1434},
diff --git a/src/main/python/trec-covid/generate_round5_baselines.py b/src/main/python/trec-covid/generate_round5_baselines.py
index 7f569de44d..cf6f8f0055 100644
--- a/src/main/python/trec-covid/generate_round5_baselines.py
+++ b/src/main/python/trec-covid/generate_round5_baselines.py
@@ -89,9 +89,9 @@ def main():
     if not (os.path.isdir(indexes[0]) and os.path.isdir(indexes[1]) and os.path.isdir(indexes[2])):
         print('Required indexes do not exist. Please download first.')
 
-    round4_cumulative_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round4-cumulative.txt'
-    complete_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-complete.txt'
-    round5_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round5.txt'
+    round4_cumulative_qrels = 'tools/topics-and-qrels/qrels.covid-round4-cumulative.txt'
+    complete_qrels = 'tools/topics-and-qrels/qrels.covid-complete.txt'
+    round5_qrels = 'tools/topics-and-qrels/qrels.covid-round5.txt'
 
     # MD5 checksums don't match anymore, see https://github.com/castorini/anserini/issues/1669
     check_md5_flag = False
@@ -103,11 +103,11 @@ def main():
 
     expected_metrics = {
         'anserini.covid-r5.abstract.qq.bm25.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.4580, 'judged_cut_10': 0.5880, 'ndcg_cut_20': 0.4379,
-             'judged_cut_20': 0.5940, 'map': 0.1903, 'recall_1000': 0.4525, 'judged_cut_1000': 0.2264},
+            {'topics': 50, 'ndcg_cut_10': 0.4569, 'judged_cut_10': 0.5860, 'ndcg_cut_20': 0.4417,
+             'judged_cut_20': 0.5930, 'map': 0.1904, 'recall_1000': 0.4525, 'judged_cut_1000': 0.2264},
         'anserini.covid-r5.abstract.qdel.bm25.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.4912, 'judged_cut_10': 0.6240, 'ndcg_cut_20': 0.4596,
-             'judged_cut_20': 0.6040, 'map': 0.2042, 'recall_1000': 0.4714, 'judged_cut_1000': 0.2351},
+            {'topics': 50, 'ndcg_cut_10': 0.4903, 'judged_cut_10': 0.6180, 'ndcg_cut_20': 0.4597,
+             'judged_cut_20': 0.6030, 'map': 0.2041, 'recall_1000': 0.4714, 'judged_cut_1000': 0.2351},
         'anserini.covid-r5.full-text.qq.bm25.txt':
             {'topics': 50, 'ndcg_cut_10': 0.3240, 'judged_cut_10': 0.5660, 'ndcg_cut_20': 0.3055,
              'judged_cut_20': 0.5250, 'map': 0.1324, 'recall_1000': 0.3758, 'judged_cut_1000': 0.2171},
@@ -115,30 +115,30 @@ def main():
             {'topics': 50, 'ndcg_cut_10': 0.4634, 'judged_cut_10': 0.6460, 'ndcg_cut_20': 0.4387,
              'judged_cut_20': 0.6280, 'map': 0.1793, 'recall_1000': 0.4368, 'judged_cut_1000': 0.2425},
         'anserini.covid-r5.paragraph.qq.bm25.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.4077, 'judged_cut_10': 0.6160, 'ndcg_cut_20': 0.3907,
-             'judged_cut_20': 0.5920, 'map': 0.1981, 'recall_1000': 0.4877, 'judged_cut_1000': 0.2661},
+            {'topics': 50, 'ndcg_cut_10': 0.4061, 'judged_cut_10': 0.6160, 'ndcg_cut_20': 0.3900,
+             'judged_cut_20': 0.5910, 'map': 0.1980, 'recall_1000': 0.4877, 'judged_cut_1000': 0.2661},
         'anserini.covid-r5.paragraph.qdel.bm25.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.4918, 'judged_cut_10': 0.6440, 'ndcg_cut_20': 0.4569,
-             'judged_cut_20': 0.6250, 'map': 0.2163, 'recall_1000': 0.5101, 'judged_cut_1000': 0.2710},
+            {'topics': 50, 'ndcg_cut_10': 0.4905, 'judged_cut_10': 0.6440, 'ndcg_cut_20': 0.4569,
+             'judged_cut_20': 0.6250, 'map': 0.2163, 'recall_1000': 0.5099, 'judged_cut_1000': 0.2710},
         'anserini.covid-r5.fusion1.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.4696, 'judged_cut_10': 0.6520, 'ndcg_cut_20': 0.4539,
-             'judged_cut_20': 0.6490, 'map': 0.2044, 'recall_1000': 0.5027, 'judged_cut_1000': 0.2751},
+            {'topics': 50, 'ndcg_cut_10': 0.4696, 'judged_cut_10': 0.6540, 'ndcg_cut_20': 0.4525,
+             'judged_cut_20': 0.6500, 'map': 0.2042, 'recall_1000': 0.5027, 'judged_cut_1000': 0.2750},
         'anserini.covid-r5.fusion2.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.5077, 'judged_cut_10': 0.6800, 'ndcg_cut_20': 0.4956,
-             'judged_cut_20': 0.6690, 'map': 0.2304, 'recall_1000': 0.5378, 'judged_cut_1000': 0.2851},
+            {'topics': 50, 'ndcg_cut_10': 0.5057, 'judged_cut_10': 0.6800, 'ndcg_cut_20': 0.4954,
+             'judged_cut_20': 0.6690, 'map': 0.2303, 'recall_1000': 0.5377, 'judged_cut_1000': 0.2851},
         'anserini.covid-r5.abstract.qdel.bm25+rm3Rf.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.6177, 'judged_cut_10': 0.6620, 'ndcg_cut_20': 0.5738,
-             'judged_cut_20': 0.6510, 'map': 0.2657, 'recall_1000': 0.5505, 'judged_cut_1000': 0.2562},
+            {'topics': 50, 'ndcg_cut_10': 0.6207, 'judged_cut_10': 0.6560, 'ndcg_cut_20': 0.5782,
+             'judged_cut_20': 0.6470, 'map': 0.2656, 'recall_1000': 0.5509, 'judged_cut_1000': 0.2563},
     }
     evaluate_runs(round4_cumulative_qrels, cumulative_runs, expected=expected_metrics, check_md5=check_md5_flag)
 
     expected_metrics = {
         'anserini.covid-r5.abstract.qq.bm25.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.6925, 'judged_cut_10': 0.9740, 'ndcg_cut_20': 0.6586,
-             'judged_cut_20': 0.9700, 'map': 0.3010, 'recall_1000': 0.4636, 'judged_cut_1000': 0.4159},
+            {'topics': 50, 'ndcg_cut_10': 0.6899, 'judged_cut_10': 0.9760, 'ndcg_cut_20': 0.6557,
+             'judged_cut_20': 0.9700, 'map': 0.3009, 'recall_1000': 0.4636, 'judged_cut_1000': 0.4159},
         'anserini.covid-r5.abstract.qdel.bm25.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.7301, 'judged_cut_10': 0.9980, 'ndcg_cut_20': 0.6979,
-             'judged_cut_20': 0.9900, 'map': 0.3230, 'recall_1000': 0.4839, 'judged_cut_1000': 0.4286},
+            {'topics': 50, 'ndcg_cut_10': 0.7260, 'judged_cut_10': 0.9960, 'ndcg_cut_20': 0.6975,
+             'judged_cut_20': 0.9900, 'map': 0.3229, 'recall_1000': 0.4838, 'judged_cut_1000': 0.4286},
         'anserini.covid-r5.full-text.qq.bm25.txt':
             {'topics': 50, 'ndcg_cut_10': 0.4709, 'judged_cut_10': 0.8920, 'ndcg_cut_20': 0.4382,
              'judged_cut_20': 0.8370, 'map': 0.1777, 'recall_1000': 0.3427, 'judged_cut_1000': 0.3397},
@@ -146,39 +146,39 @@ def main():
             {'topics': 50, 'ndcg_cut_10': 0.6286, 'judged_cut_10': 0.9840, 'ndcg_cut_20': 0.5973,
              'judged_cut_20': 0.9630, 'map': 0.2391, 'recall_1000': 0.4087, 'judged_cut_1000': 0.3875},
         'anserini.covid-r5.paragraph.qq.bm25.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.5832, 'judged_cut_10': 0.9600, 'ndcg_cut_20': 0.5659,
+            {'topics': 50, 'ndcg_cut_10': 0.5832, 'judged_cut_10': 0.9600, 'ndcg_cut_20': 0.5656,
              'judged_cut_20': 0.9390, 'map': 0.2808, 'recall_1000': 0.4695, 'judged_cut_1000': 0.4412},
         'anserini.covid-r5.paragraph.qdel.bm25.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.6764, 'judged_cut_10': 0.9840, 'ndcg_cut_20': 0.6368,
+            {'topics': 50, 'ndcg_cut_10': 0.6764, 'judged_cut_10': 0.9840, 'ndcg_cut_20': 0.6367,
              'judged_cut_20': 0.9740, 'map': 0.3089, 'recall_1000': 0.4949, 'judged_cut_1000': 0.4542},
         'anserini.covid-r5.fusion1.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.6469, 'judged_cut_10': 0.9860, 'ndcg_cut_20': 0.6184,
-             'judged_cut_20': 0.9800, 'map': 0.2952, 'recall_1000': 0.4967, 'judged_cut_1000': 0.4675},
+            {'topics': 50, 'ndcg_cut_10': 0.6488, 'judged_cut_10': 0.9860, 'ndcg_cut_20': 0.6190,
+             'judged_cut_20': 0.9800, 'map': 0.2952, 'recall_1000': 0.4966, 'judged_cut_1000': 0.4674},
         'anserini.covid-r5.fusion2.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.6972, 'judged_cut_10': 1.0000, 'ndcg_cut_20': 0.6785,
+            {'topics': 50, 'ndcg_cut_10': 0.6946, 'judged_cut_10': 1.0000, 'ndcg_cut_20': 0.6787,
              'judged_cut_20': 1.000, 'map': 0.3329, 'recall_1000': 0.5313, 'judged_cut_1000': 0.4869},
         'anserini.covid-r5.abstract.qdel.bm25+rm3Rf.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.8395, 'judged_cut_10': 1.0000, 'ndcg_cut_20': 0.7955,
-             'judged_cut_20': 0.9990, 'map': 0.3911, 'recall_1000': 0.5536, 'judged_cut_1000': 0.4607},
+            {'topics': 50, 'ndcg_cut_10': 0.8406, 'judged_cut_10': 1.0000, 'ndcg_cut_20': 0.7965,
+             'judged_cut_20': 1.000, 'map': 0.3912, 'recall_1000': 0.5540, 'judged_cut_1000': 0.4610},
     }
     evaluate_runs(complete_qrels, cumulative_runs, expected=expected_metrics, check_md5=check_md5_flag)
 
     expected_metrics = {
         'anserini.final-r5.fusion1.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.5668, 'judged_cut_10': 0.9140, 'ndcg_cut_20': 0.5244,
-             'judged_cut_20': 0.8490, 'map': 0.2302, 'recall_1000': 0.5615, 'judged_cut_1000': 0.2148},
+            {'topics': 50, 'ndcg_cut_10': 0.5665, 'judged_cut_10': 0.9140, 'ndcg_cut_20': 0.5247,
+             'judged_cut_20': 0.8490, 'map': 0.2302, 'recall_1000': 0.5616, 'judged_cut_1000': 0.2149},
         'anserini.final-r5.fusion1.post-processed.txt':
             {'topics': 50, 'ndcg_cut_10': 0.5726, 'judged_cut_10': 0.9240, 'ndcg_cut_20': 0.5313,
              'judged_cut_20': 0.8570, 'map': 0.2314, 'recall_1000': 0.5615, 'judged_cut_1000': 0.2151},
         'anserini.final-r5.fusion2.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.6366, 'judged_cut_10': 0.9640, 'ndcg_cut_20': 0.5941,
-             'judged_cut_20': 0.9080, 'map': 0.2716, 'recall_1000': 0.6012, 'judged_cut_1000': 0.2263},
+            {'topics': 50, 'ndcg_cut_10': 0.6387, 'judged_cut_10': 0.9620, 'ndcg_cut_20': 0.5955,
+             'judged_cut_20': 0.9090, 'map': 0.2719, 'recall_1000': 0.6013, 'judged_cut_1000': 0.2263},
         'anserini.final-r5.fusion2.post-processed.txt':
             {'topics': 50, 'ndcg_cut_10': 0.6474, 'judged_cut_10': 0.9780, 'ndcg_cut_20': 0.6007,
              'judged_cut_20': 0.9150, 'map': 0.2734, 'recall_1000': 0.6012, 'judged_cut_1000': 0.2267},
         'anserini.final-r5.rf.txt':
-            {'topics': 50, 'ndcg_cut_10': 0.7777, 'judged_cut_10': 0.9680, 'ndcg_cut_20': 0.7193,
-             'judged_cut_20': 0.9270, 'map': 0.3235, 'recall_1000': 0.6378, 'judged_cut_1000': 0.2197},
+            {'topics': 50, 'ndcg_cut_10': 0.7789, 'judged_cut_10': 0.9700, 'ndcg_cut_20': 0.7188,
+             'judged_cut_20': 0.9270, 'map': 0.3234, 'recall_1000': 0.6378, 'judged_cut_1000': 0.2197},
         'anserini.final-r5.rf.post-processed.txt':
             {'topics': 50, 'ndcg_cut_10': 0.7944, 'judged_cut_10': 0.9860, 'ndcg_cut_20': 0.7346,
              'judged_cut_20': 0.9470, 'map': 0.3280, 'recall_1000': 0.6378, 'judged_cut_1000': 0.2201},
diff --git a/src/main/python/trec-covid/generate_round5_doc2query_baselines.py b/src/main/python/trec-covid/generate_round5_doc2query_baselines.py
index 97e97a9628..de88990932 100644
--- a/src/main/python/trec-covid/generate_round5_doc2query_baselines.py
+++ b/src/main/python/trec-covid/generate_round5_doc2query_baselines.py
@@ -87,8 +87,8 @@
 
 
 def perform_runs():
-    base_topics = 'src/main/resources/topics-and-qrels/topics.covid-round5.xml'
-    udel_topics = 'src/main/resources/topics-and-qrels/topics.covid-round5-udel.xml'
+    base_topics = 'tools/topics-and-qrels/topics.covid-round5.xml'
+    udel_topics = 'tools/topics-and-qrels/topics.covid-round5-udel.xml'
 
     print('')
     print('## Running on abstract index...')
@@ -109,7 +109,7 @@ def perform_runs():
     os.system(f'target/appassembler/bin/SearchCollection -index {abstract_index} ' +
               f'-topicreader Covid -topics {udel_topics} -topicfield query -removedups ' +
               f'-bm25 -rm3 -rm3.fbTerms 100 -hits 10000 ' +
-              f'-rf.qrels src/main/resources/topics-and-qrels/qrels.covid-round4-cumulative.txt ' +
+              f'-rf.qrels tools/topics-and-qrels/qrels.covid-round4-cumulative.txt ' +
               f'-output runs/{abstract_prefix}.qdel.bm25+rm3Rf.txt -runtag {abstract_prefix}.qdel.bm25+rm3Rf.txt')
 
     print('')
@@ -222,9 +222,9 @@ def main():
     if not (os.path.isdir(indexes[0]) and os.path.isdir(indexes[1]) and os.path.isdir(indexes[2])):
         print('Required indexes do not exist. Please download first.')
 
-    round4_cumulative_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round4-cumulative.txt'
-    complete_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-complete.txt'
-    round5_qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round5.txt'
+    round4_cumulative_qrels = 'tools/topics-and-qrels/qrels.covid-round4-cumulative.txt'
+    complete_qrels = 'tools/topics-and-qrels/qrels.covid-complete.txt'
+    round5_qrels = 'tools/topics-and-qrels/qrels.covid-round5.txt'
 
     # MD5 checksums don't match anymore, see https://github.com/castorini/anserini/issues/1669
     check_md5_flag = False
diff --git a/src/main/python/trec-covid/index_cord19.py b/src/main/python/trec-covid/index_cord19.py
index 652695e3dd..869052d369 100644
--- a/src/main/python/trec-covid/index_cord19.py
+++ b/src/main/python/trec-covid/index_cord19.py
@@ -113,7 +113,7 @@ def build_indexes(date):
 
 
 def evaluate_run(run):
-    qrels = 'src/main/resources/topics-and-qrels/qrels.covid-round3-cumulative.txt'
+    qrels = 'tools/topics-and-qrels/qrels.covid-round3-cumulative.txt'
     metrics = {}
     output = subprocess.check_output(
         f'tools/eval/trec_eval.9.0.4/trec_eval -c -m ndcg_cut.10 {qrels} runs/{run}', shell=True)
@@ -131,8 +131,8 @@ def evaluate_run(run):
 
 
 def verify_indexes(date):
-    topics = 'src/main/resources/topics-and-qrels/topics.covid-round3.xml'
-    whitelist = 'src/main/resources/topics-and-qrels/docids.covid.round3.txt'
+    topics = 'tools/topics-and-qrels/topics.covid-round3.xml'
+    whitelist = 'tools/topics-and-qrels/docids.covid.round3.txt'
 
     print('Verifying abstract index...')
     abstract_index = f'indexes/lucene-index-cord19-abstract-{date} '