Merge pull request #209 from broadinstitute/dev_to_main

prepare for main merge
broadinstitute · Mar 22, 2024 · c012907 · c012907
2 parents 8dcc2e1 + 1b5affb
commit c012907
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diff --git a/.gitignore b/.gitignore
@@ -3,6 +3,7 @@ results/
 tests/test_output
 tests/**/Metrics
 docs/_build/*
+config/config_biosamples.tsv
 # emacs backups
 *~
 

diff --git a/config/config.yaml b/config/config.yaml
@@ -31,7 +31,9 @@ params_candidate:
 
 # These parameters are used to run the Run Neighborhoods portion of the abc code
 params_neighborhoods:
-        use_qnorm: True
+        # Recommended to keep as True. Setting to False leads will result in 
+        # different ABC scores that don't follow the pre-set ABC thresholds
+        use_qnorm: True  
 
 # These parameters are used to run the Predictions portion of the abc code
 params_predict:

diff --git a/config/config_biosamples.tsv b/config/config_biosamples.tsv
diff --git a/reference/hg19/CollapsedGeneBounds.hg19.TSS500bp.bed b/reference/hg19/CollapsedGeneBounds.hg19.TSS500bp.bed
diff --git a/reference/hg19/CollapsedGeneBounds.hg19.bed b/reference/hg19/CollapsedGeneBounds.hg19.bed