fix ac_loci_gc input

nf-core · Feb 25, 2020 · d1e9846 · d1e9846
1 parent 0794202
commit d1e9846
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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"