removed broken paths

Author: sprokopec

scripts/fragmentomics/griffin/site_configs/Immune_Calderon_sites.yaml

@@ -39,4 +39,3 @@ site_files:
   Th17_precursors: /cluster/projects/pughlab/bin/Griffin/sites/Immune_Calderon/Th17_precursors_hg38.high_mapability.txt
   Th1_precursors: /cluster/projects/pughlab/bin/Griffin/sites/Immune_Calderon/Th1_precursors_hg38.high_mapability.txt
   Th2_precursors: /cluster/projects/pughlab/bin/Griffin/sites/Immune_Calderon/Th2_precursors_hg38.high_mapability.txt
-  stop: /cluster/projects/pughlab/bin/Griffin/sites/stop.txt

scripts/fragmentomics/griffin/site_configs/Immune_sites.yaml

@@ -12,4 +12,3 @@ site_files:
   T_helper1_cell: /cluster/projects/pughlab/bin/Griffin/sites/Immune/T_helper1_cell_hg38.txt
   T_helper2_cell: /cluster/projects/pughlab/bin/Griffin/sites/Immune/T_helper2_cell_hg38.txt
   T_reg_cell: /cluster/projects/pughlab/bin/Griffin/sites/Immune/T_reg_cell_hg38.txt
-  stop: /cluster/projects/pughlab/bin/Griffin/stop.txt

scripts/fragmentomics/griffin/site_configs/LFS_sites.yaml

@@ -4,4 +4,3 @@ site_files:
   EZH2_targets: /cluster/projects/pughlab/bin/Griffin/sites/LFS/EZH2_targets_TSS_hg38.high_mapability.txt
   H3K27me3: /cluster/projects/pughlab/bin/Griffin/sites/LFS/H3K27me3_TSS_hg38.high_mapability.txt
   TP53_DMR: /cluster/projects/pughlab/bin/Griffin/sites/LFS/TP53_DMR_hg38.high_mapability.txt
-  stop: /cluster/projects/pughlab/bin/Griffin/stop.txt

scripts/fragmentomics/griffin/site_configs/TFBS_Ulz_sites.yaml

@@ -503,4 +503,3 @@ site_files:
   ZSCAN5A: /cluster/projects/pughlab/bin/Griffin/sites/TFBS_Ulz/ZSCAN5A_Top1000_hg38.high_mapability.txt
   ZSCAN5D: /cluster/projects/pughlab/bin/Griffin/sites/TFBS_Ulz/ZSCAN5D_Top1000_hg38.high_mapability.txt
   ZXDC: /cluster/projects/pughlab/bin/Griffin/sites/TFBS_Ulz/ZXDC_Top1000_hg38.high_mapability.txt
-  stop: /cluster/projects/pughlab/bin/Griffin/sites/stop.txt

scripts/fragmentomics/griffin/site_configs/TP53_sites.yaml

@@ -9,4 +9,3 @@ site_files:
   TP53_targets_StopCodon: /cluster/projects/pughlab/bin/Griffin/sites/TP53/tp53_StopCodon_hg38.high_mapability.txt
   TP53_targets_TSS: /cluster/projects/pughlab/bin/Griffin/sites/TP53/tp53_TSS_hg38.high_mapability.txt
   TP53_targets_TSE: /cluster/projects/pughlab/bin/Griffin/sites/TP53/tp53_TSE_hg38.high_mapability.txt
-  stop: /cluster/projects/pughlab/bin/Griffin/stop.txt

scripts/fragmentomics/griffin/site_configs/hematopoietic_sites.yaml

@@ -1,3 +1,2 @@
 site_files:
   hematopoietic: /cluster/projects/pughlab/bin/Griffin/sites/hematopoietic/Hematopoietic_hg38.txt
-  stop: /cluster/projects/pughlab/bin/Griffin/sites/stop.high_mapability.txt

scripts/fragmentomics/griffin/site_configs/uveal_sites.yaml

@@ -3,4 +3,3 @@ site_files:
   Liver_atac: /cluster/projects/pughlab/bin/Griffin/sites/uveal/liver_atac_merged.high_mapability.txt
   Liver_dnase: /cluster/projects/pughlab/bin/Griffin/sites/uveal/liver_dnase_merged.high_mapability.txt
   Liver_hg38: /cluster/projects/pughlab/bin/Griffin/sites/uveal/liver_hg38_merged.high_mapability.txt
-  stop: /cluster/projects/pughlab/bin/Griffin/sites/uveal/stop.high_mapability.txt