Merge pull request #210 from broadinstitute/dev

Dev
broadinstitute · Mar 23, 2024 · dd637b6 · dd637b6
2 parents 8345d2f + c012907
commit dd637b6
Show file tree

Hide file tree

Showing 38 changed files with 94,784 additions and 56,853 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -34,12 +34,14 @@ jobs:
             black . --check
       - run:
           name: Install abc-env
+          no_output_timeout: 30m
           command: |
             mamba env create -f workflow/envs/abcenv.yml
       - run:
           name: Run tests
+          no_output_timeout: 30m
           command: |
-            conda run -n abc-env pytest
+            conda run -n abc-env pytest -n 4
       - slack/notify:
           branch_pattern: dev,main 
           channel: abc_circleci

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/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