updated default config

UMCUGenetics · Jul 10, 2020 · a527412 · a527412
1 parent 75f8997
commit a527412
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Showing 2 changed files with 14 additions and 14 deletions.
diff --git a/configs/resources.config b/configs/resources.config
@@ -4,18 +4,18 @@ params {
     "GRCh37" {
       fasta = "${params.resource_dir}/GRCh37/Sequence/genome.fa"
       gatk_known_sites = [
-        "${params.resource_dir}/GRCh37/Annotation/1000G_phase1.indels.b37.vcf.gz",
-        "${params.resource_dir}/GRCh37/Annotation/dbsnp_138.b37.vcf.gz",
-        "${params.resource_dir}/GRCh37/Annotation/Mills_and_1000G_gold_standard.indels.b37.vcf.gz"
+        "${params.resource_dir}/GRCh37/Annotation/1000G/1000G_phase1.indels.b37.vcf.gz",
+        "${params.resource_dir}/GRCh37/Annotation/dbsnp/dbsnp_138.b37.vcf.gz",
+        "${params.resource_dir}/GRCh37/Annotation/1000G/Mills_and_1000G_gold_standard.indels.b37.vcf.gz"
       ]
-      dbsnp = "${params.resource_dir}/GRCh37/Annotation/dbsnp_138.b37.vcf.gz"
-      dbnsfp = "${params.resource_dir}/GRCh37/Annotation/dbNSFP2.9.3.txt.gz"
-      cosmic = "${params.resource_dir}/GRCh37/Annotation/CosmicCodingMuts_v80.vcf.gz"
-      gonl = "${params.resource_dir}/GRCh37/Annotation/gonl.snps_indels.r5.vcf.gz"
+      dbsnp = "${params.resource_dir}/GRCh37/Annotation/dbsnp/dbsnp_138.b37.vcf.gz"
+      dbnsfp = "${params.resource_dir}/GRCh37/Annotation/dbNSFP/dbNSFP2.9.3.txt.gz"
+      cosmic = "${params.resource_dir}/GRCh37/Annotation/Cosmic/CosmicCodingMuts_v80.vcf.gz"
+      gonl = "${params.resource_dir}/GRCh37/Annotation/GoNL/gonl.snps_indels.r5.vcf.gz"
       interval_list = "${params.resource_dir}/GRCh37/Sequence/genome.interval_list"
       freec_chr_len = "${params.resource_dir}/GRCh37/Sequence/genome.len"
       freec_chr_files = "${params.resource_dir}/GRCh37/Sequence/chr_files"
-      freec_mappability = "${params.resource_dir}/GRCh37/Annotation/out100m2_hg19.gem"
+      freec_mappability = "${params.resource_dir}/GRCh37/Annotation/misc/out100m2_hg19.gem"
     }
     "UMD3.1" {
       fasta = "${params.resource_dir}/UMD3.1/Sequence/Bos_taurus.UMD3.1.dna.toplevel.fa"

diff --git a/configs/test-run.config b/configs/test-run.config
@@ -1,7 +1,7 @@
 /* Always include process and resources config */
-includeConfig '/home/cog/sboymans/scripts/NF-IAP_dev/configs/nextflow.config'
-includeConfig '/home/cog/sboymans/scripts/NF-IAP_dev/configs/process.config'
-includeConfig '/home/cog/sboymans/scripts/NF-IAP_dev/configs/resources.config'
+includeConfig '/home/cog/sboymans/scripts/NF-IAP/configs/nextflow.config'
+includeConfig '/home/cog/sboymans/scripts/NF-IAP/configs/process.config'
+includeConfig '/home/cog/sboymans/scripts/NF-IAP/configs/resources.config'
 
 params {
   help = false
@@ -11,12 +11,12 @@ params {
   vcf_path = ''
   genome = 'GRCh37'
 
-  premapQC = false
-  postmapQC = false
+  premapQC = true
+  postmapQC = true
   germlineCalling = true
   variantFiltration = true
   variantAnnotation = true
   svCalling = false
   cnvCalling = false
-  splitVCF = true
+  //splitVCF = true
 }