fix: change hg19 reference intervals

CCBR · May 23, 2024 · 21133f7 · 21133f7
1 parent 60a359b
commit 21133f7
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Showing 3 changed files with 3 additions and 4 deletions.
diff --git a/conf/genomes.config b/conf/genomes.config
@@ -43,7 +43,7 @@ params {
             genomefai = "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19.with_extra.fa.fai"
             bwagenome= "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa"
             genomedict= "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.dict"
-            intervals= "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/hg19_noblacklist.bed"
+            intervals= "/data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg19/hg19_noblacklist_maincontig.bed"
             INDELREF = "/fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf" //ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz" 
             KNOWNINDELS = "-known /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -known /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf"
             KNOWNRECAL = '--known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/dbsnp_138.hg38.vcf.gz --known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GATK_resource_bundle/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz'

diff --git a/modules/local/variant_calling_tonly.nf b/modules/local/variant_calling_tonly.nf
@@ -338,8 +338,7 @@ process octopus_tonly {
     """
     octopus -R $GENOMEREF -C cancer -I ${tumor} \
     --annotations AF AC AD DP \
-    --target-working-memory 92Gb \
-    -B 90Gb \
+    -B 92Gb \
     -t ${bed} \
     --threads ${task.cpus}\
     $SOMATIC_FOREST \

diff --git a/subworkflows/local/workflows.nf b/subworkflows/local/workflows.nf
@@ -393,7 +393,7 @@ workflow VC {
             | annotvep_tn_combined
     }
 
-
+    
     //Implement PCGR Annotator/CivIC Next
         if ("octopus" in call_list){
            somaticcall_input=octopus_in_sc