Update comments and filepaths for chain_file and repeat_bed

uclahs-cds · Jul 15, 2024 · ff151c8 · ff151c8
1 parent cf0a904
commit ff151c8
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Showing 2 changed files with 11 additions and 7 deletions.
diff --git a/config/template.config b/config/template.config
@@ -32,12 +32,12 @@ params {
     // params.funcotator_data.dest_reference_id
     dest_fasta_ref = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
 
-    // The liftover chain file between the source and destination FASTAS
+    // The liftover chain file between the source and destination FASTA
     // references
     chain_file = "/hot/ref/tool-specific-input/liftOver/hg19ToHg38.over.chain"
 
-    // FIXME Update to a stable path under /hot/ref/database
-    repeat_bed = "/hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/intervals/GRCh38_RepeatMasker_intervals.bed"
+    // FIXME How to describe this file?
+    repeat_bed = "/hot/ref/database/RepeatMasker-v3.1.0/processed/GRCh38/GRCh38_RepeatMasker_intervals.bed"
 }
 
 // Setup the pipeline config. DO NOT REMOVE THIS LINE!

diff --git a/test/nftest.config b/test/nftest.config
@@ -18,15 +18,19 @@ params {
         dest_reference_id = "hg38"
     }
 
-    // The source reference sequence (FASTA)
+    // The source reference sequence (FASTA). Must correspond with
+    // params.funcotator_data.src_reference_id
     src_fasta_ref = "/hot/ref/reference/GRCh37-EBI-hs37d5/hs37d5.fa"
 
-    // The destination reference sequence (FASTA)
+    // The destination reference sequence (FASTA). Must correspond with
+    // params.funcotator_data.dest_reference_id
     dest_fasta_ref = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
 
-    chain_file = "/hot/resource/genomics/liftover_chain_files/hg19ToHg38.over.chain"
+    // The liftover chain file between the source and destination FASTA
+    // references
+    chain_file = "/hot/ref/tool-specific-input/liftOver/hg19ToHg38.over.chain"
 
-    repeat_bed = "/hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/intervals/GRCh38_RepeatMasker_intervals.bed"
+    repeat_bed = "/hot/ref/database/RepeatMasker-v3.1.0/processed/GRCh38/GRCh38_RepeatMasker_intervals.bed"
 }
 
 // Setup the pipeline config. DO NOT REMOVE THIS LINE!