Merge pull request #210 from broadinstitute/dev

Dev

Author: atancoder

.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

.gitignore

@@ -3,6 +3,7 @@ results/
 tests/test_output
 tests/**/Metrics
 docs/_build/*
+config/config_biosamples.tsv
 # emacs backups
 *~
 

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:

reference/hg19/CollapsedGeneBounds.hg19.TSS500bp.bed

@@ -0,0 +1,25 @@
+chr1	249250621
+chr2	243199373
+chr3	198022430
+chr4	191154276
+chr5	180915260
+chr6	171115067
+chr7	159138663
+chr8	146364022
+chr9	141213431
+chr10	135534747
+chr11	135006516
+chr12	133851895
+chr13	115169878
+chr14	107349540
+chr15	102531392
+chr16	90354753
+chr17	81195210
+chr18	78077248
+chr19	59128983
+chr20	63025520
+chr21	48129895
+chr22	51304566
+chrX	155270560
+chrY	59373566
+chrM	16571

reference/hg19/CollapsedGeneBounds.hg19.bed

@@ -16043,7 +16043,6 @@ chr17	36089910	36090410	CCL3	0	-	ENSG00000277632	protein_coding
 chr17	36103576	36104076	CCL4	0	+	ENSG00000275302	protein_coding
 chr17	36196498	36196998	CCL3L3	0	-	ENSG00000276085	protein_coding
 chr17	36210812	36211312	CCL4L2	0	+	ENSG00000276070	protein_coding
-chr17_KI270909v1_alt	252216	252716	CCL3L1	0	-	ENSG00000276085	protein_coding
 chr17	36439305	36439805	TBC1D3B	0	-	ENSG00000274808	protein_coding
 chr17	36486376	36486876	ZNHIT3	0	+	ENSG00000273611	protein_coding
 chr17	36535207	36535707	MYO19	0	-	ENSG00000278259	protein_coding