From e8ec373c261fdb34919375bac005f8d9f08fe707 Mon Sep 17 00:00:00 2001
From: nkwang <nkwang@mednet.ucla.edu>
Date: Fri, 18 Oct 2024 17:04:18 -0700
Subject: [PATCH] move resource params to methods.config

---
 config/methods.config  | 18 +++++++++++++++++-
 config/template.config | 17 -----------------
 2 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/config/methods.config b/config/methods.config
index cedd8b5..7a8ea71 100644
--- a/config/methods.config
+++ b/config/methods.config
@@ -50,7 +50,12 @@ methods {
             'dest_fasta_id',
             'dest_fasta_ref',
             'dest_fasta_fai',
-            'dest_fasta_dict'
+            'dest_fasta_dict',
+            'chain_file',
+            'repeat_bed',
+            'header_contigs',
+            'funcotator_data_source',
+            'gnomad_rds'
         ]
 
         for (key in advanced_parameters) {
@@ -71,12 +76,20 @@ methods {
 
                 params.dest_fasta_id = 'GRCh38'
                 params.dest_fasta_ref = params.fasta_ref_38
+
+                params.chain_file = params.resource_bundle_path + "/hg19ToHg38.over.chain"
+                params.repeat_bed = params.resource_bundle_path + "/GRCh38_RepeatMasker-intervals.bed"
+                params.header_contigs = params.resource_bundle_path + "/GRCh38_VCF-header-contigs.txt"
             } else {
                 params.src_fasta_id = 'GRCh38'
                 params.src_fasta_ref = params.fasta_ref_38
 
                 params.dest_fasta_id = 'GRCh37'
                 params.dest_fasta_ref = params.fasta_ref_37
+
+                params.chain_file = params.resource_bundle_path + "/hg38ToHg19.over.chain"
+                params.repeat_bed = params.resource_bundle_path + "/GRCh37_RepeatMasker-intervals.bed"
+                params.header_contigs = params.resource_bundle_path + "/GRCh37_VCF-header-contigs.txt"
             }
 
             params.src_fasta_fai = params.src_fasta_ref + ".fai"
@@ -84,6 +97,9 @@ methods {
 
             params.src_fasta_dict = Nextflow.file(params.src_fasta_ref).resolveSibling(Nextflow.file(params.src_fasta_ref).getBaseName() + '.dict').toString()
             params.dest_fasta_dict = Nextflow.file(params.dest_fasta_ref).resolveSibling(Nextflow.file(params.dest_fasta_ref).getBaseName() + '.dict').toString()
+
+            params.funcotator_data_source = params.resource_bundle_path + "/funcotator_dataSources.v1.7.20200521s_StableLift"
+            params.gnomad_rds = params.resource_bundle_path + "/gnomad.v4.0.sv.Rds"
         }
     }
 
diff --git a/config/template.config b/config/template.config
index ab6c69e..ee5778d 100644
--- a/config/template.config
+++ b/config/template.config
@@ -39,23 +39,6 @@ params {
     // Optional parameter specifying number of cpus to use for parsing large VCFs
     // Defaults to 4 if unset
     // extract_features_cpus = 4
-
-    // LiftOver chain file
-    chain_file = liftover_direction == "GRCh37ToGRCh38" ? 
-        "${resource_bundle_path}/hg19ToHg38.over.chain" : 
-        "${resource_bundle_path}/hg38ToHg19.over.chain"
-
-    // SNV required references
-    funcotator_data_source = "${resource_bundle_path}/funcotator_dataSources.v1.7.20200521s_StableLift"
-    repeat_bed = liftover_direction == "GRCh37ToGRCh38" ? 
-        "${resource_bundle_path}/GRCh38_RepeatMasker-intervals.bed" : 
-        "${resource_bundle_path}/GRCh37_RepeatMasker-intervals.bed"
-
-    // SV required references
-    gnomad_rds = "${resource_bundle_path}/gnomad.v4.0.sv.Rds"
-    header_contigs = liftover_direction == "GRCh37ToGRCh38" ? 
-        "${resource_bundle_path}/GRCh38_VCF-header-contigs.txt" : 
-        "${resource_bundle_path}/GRCh37_VCF-header-contigs.txt"
 }
 
 // Setup the pipeline config. DO NOT REMOVE THIS LINE!