From 8bdd86d96bd3d81c44be626061fdced1adfb8850 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Thu, 30 May 2024 09:58:54 -0400 Subject: [PATCH] fix: add correct references --- conf/genomes.config | 4 ++-- modules/local/copynumber.nf | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/conf/genomes.config b/conf/genomes.config index b6a0db7..3c864de 100644 --- 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 index a9fb40b..4a00109 100644 --- 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)