Merge pull request #985 from mskcc/bugfix/svcircos_intermediates

define intermediates_dir for rmarkdown rendering
mskcc · May 6, 2023 · b574758 · b574758
2 parents 0575206 + 28ee579
commit b574758
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/containers/biocircos/generate_biocircos.R b/containers/biocircos/generate_biocircos.R
@@ -145,4 +145,5 @@ gen.plot.biocircos <- function(bedpe,cnv,sample_name,genome_v){
 }
 
 plot.biocircos <- gen.plot.biocircos(bedpe=bedpe,cnv=cnv,sample_name = opt$sampleName, genome_v=genome_v )
-rmarkdown::render("biocircos.Rmd", "all", paste0(opt$sampleName,".circos.html"), output_dir='.')
+rmarkdown::render("biocircos.Rmd", "all", paste0(opt$sampleName,".circos.html"), output_dir='.',intermediates_dir='./tmp')
+unlink('./tmp',recursive=TRUE)