fixed a bug when generating WGS noncoding report

naumenko-sa · Jul 11, 2019 · 1cf40a6 · 1cf40a6
1 parent 6683306
commit 1cf40a6
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/cre.bcbio.custom_genome.sh b/cre.bcbio.custom_genome.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
 # crashes on qlogin node, building indexes takes time
+# still needs to download cloudbiolinux
 
 #PBS -l walltime=48:00:00,nodes=1:ppn=20
 #PBS -joe .
@@ -13,7 +14,8 @@ echo $PYTHONPATH
 
 #wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
 
-gunzip hs37d5.fa.gz
+#gunzip hs37d5.fa.gz
 
-bcbio_setup_genome.py -f hs37d5.fa -g /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_1.1.5/genomes/Hsapiens/GRCh37/rnaseq/ref-transcripts.gtf -n Hsapiens -b GRCh37d5 -i bwa star rtg -c 20
+bcbio_setup_genome.py -f hs37d5.fa -g /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_1.1.5/genomes/Hsapiens/GRCh37/rnaseq/ref-transcripts.gtf -n Hsapiens -b GRCh37d5 -i bwa -c 10
+# -i bwa star rtg
 
diff --git a/cre.vcf2db.R b/cre.vcf2db.R
@@ -119,7 +119,7 @@ create_report <- function(family, samples){
             highmed_impacts <- impacts %>% 
                 filter(variant_id == v_id, impact_severity %in% c("HIGH", "MED")) %>% 
                 select(gene, hgvsc, spliceregion)
-            if (nrow(highmed_impacts > 0)){
+            if (nrow(highmed_impacts) > 0){
                 v_impacts <- paste0(highmed_impacts$gene, ":", highmed_impacts$hgvsc, ":", 
                                 highmed_impacts$spliceregion)
                 s_impacts <- paste(v_impacts, collapse = ",")