fix blacklist populating from cookiecutter (#81)

alsmith151 · Jul 24, 2023 · 23ad7bc · 23ad7bc
1 parent 11bfe06
commit 23ad7bc
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/...tter_config/config_atac/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_atac.yml b/...tter_config/config_atac/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_atac.yml
@@ -18,7 +18,7 @@ remove_pcr_duplicates_method: "{{cookiecutter.remove_pcr_duplicates_method}}"
 shift_atac_reads: "{{cookiecutter.shift_atac_reads}}"
 
 remove_blacklist: "{{cookiecutter.remove_blacklist}}"
-blacklist: "path/to/hg38-blacklist.v2.bed.gz"
+blacklist: "{{cookiecutter.blacklist}}"
 
 make_bigwigs: "{{cookiecutter.make_bigwigs}}"  
 pileup_method: "{{cookiecutter.pileup_method}}"

diff --git a/...tter_config/config_chip/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_chip.yml b/...tter_config/config_chip/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_chip.yml
@@ -18,7 +18,7 @@ remove_pcr_duplicates_method: "{{cookiecutter.remove_pcr_duplicates_method}}"
 shift_atac_reads: "False"
 
 remove_blacklist: "{{cookiecutter.remove_blacklist}}"
-blacklist: "path/to/hg38-blacklist.v2.bed.gz"
+blacklist: "{{cookiecutter.blacklist}}"
 
 make_bigwigs: "{{cookiecutter.make_bigwigs}}"  
 pileup_method: "{{cookiecutter.pileup_method}}"

diff --git a/...cutter_config/config_rna/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_rna.yml b/...cutter_config/config_rna/{{cookiecutter.date}}_{{cookiecutter.project_id}}/config_rna.yml
@@ -22,7 +22,7 @@ remove_pcr_duplicates_method: "{{cookiecutter.remove_pcr_duplicates_method}}"
 shift_atac_reads: "False"
 
 remove_blacklist: "{{cookiecutter.remove_blacklist}}"
-blacklist: "path/to/hg38-blacklist.v2.bed.gz"
+blacklist: "{{cookiecutter.blacklist}}"
 
 make_bigwigs: "{{cookiecutter.make_bigwigs}}"  
 pileup_method: "{{cookiecutter.pileup_method}}"