fix: add correct references

CCBR · May 30, 2024 · 8bdd86d · 8bdd86d
1 parent 9892887
commit 8bdd86d
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/conf/genomes.config b/conf/genomes.config
@@ -35,7 +35,7 @@ params {
             HCBED = "-high_confidence_bed /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/hmftools/v5_34/ref/38/variants/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed.gz"
             ENSEMBLCACHE = "-ensembl_data_dir /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/hmftools/v5_34/ref/38/common/ensembl_data"
             //PURPLE
-            GERMLINEHET = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/PURPLE/GermlineHetPon.38.vcf.gz"
+            GERMLINEHET = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/hmftools/v5_34/ref/38/copy_number/AmberGermlineSites.38.tsv.gz"
             GCPROFILE = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/hmftools/v5_34/ref/38/copy_number/GC_profile.1000bp.38.cnp"
             DIPLODREG = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/hmftools/v5_34/ref/38/copy_number/DiploidRegions.38.bed.gz"
             DRIVERS = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/hmftools/v5_34/ref/38/common/DriverGenePanel.38.tsv"
@@ -75,7 +75,7 @@ params {
             HCBED = "-high_confidence_bed /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/hmftools/v5_34/ref/38/variants/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed.gz"
             ENSEMBLCACHE = "-ensembl_data_dir /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/hmftools/v5_34/ref/38/common/ensembl_data"
              //PURPLE
-            GERMLINEHET = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/PURPLE/GermlineHetPon.38.vcf.gz"
+            GERMLINEHET = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/hmftools/v5_34/ref/38/copy_number/AmberGermlineSites.38.tsv.gz"
             GCPROFILE = "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/PURPLE/GC_profile.1000bp.38.cnp"
             DIPLODREG = '/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/PURPLE/DiploidRegions.38.bed.gz'
             ENSEMBLCACHE = '/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/PURPLE/ensembl_data/'

diff --git a/modules/local/copynumber.nf b/modules/local/copynumber.nf
@@ -17,6 +17,7 @@ if (params.genome=="mm10"){
 if (params.genome=="hg38" | params.genome=="hg19"){
     GENOMEVER=params.genomes[params.genome].GENOMEVER
     GCPROFILE=file(params.genomes[params.genome].GCPROFILE)
+    GERMLINEHET=file(params.genomes[params.genome].GERMLINEHET)
     DIPLODREG=file(params.genomes[params.genome].DIPLODREG)
     ENSEMBLCACHE=params.genomes[params.genome].ENSEMBLCACHE
     DRIVERS=file(params.genomes[params.genome].DRIVERS)