diff --git a/bin/run_ascat.r b/bin/run_ascat.r index 5d531592b..d8800f91b 100755 --- a/bin/run_ascat.r +++ b/bin/run_ascat.r @@ -52,7 +52,7 @@ if(opt$gender=="XY"){ #GC wave correction -#ascat.bc = ascat.GCcorrect(ascat.bc, opt$gcfile) +ascat.bc = ascat.GCcorrect(ascat.bc, opt$gcfile) #Plot the raw data ascat.plotRawData(ascat.bc) diff --git a/conf/igenomes.config b/conf/igenomes.config index 49088ef14..3997c6903 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -11,7 +11,7 @@ params { genomes { 'GRCh37' { ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci" - ac_lociGC = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc" + ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc" bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}" chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes" chr_length = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Length/human_g1k_v37_decoy.len" @@ -31,7 +31,7 @@ params { } 'GRCh38' { ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci" - ac_lociGC = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc" + ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc" bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}" chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes" chr_length = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len"