Mercurial > repos > artbio > snvtocnv

diff sequenza_to_hrdtools_input.R @ 7:e66b91475343 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 7df896b940e80984168b1fa6326c4d862e7e208c"
author artbio
date Sun, 07 Mar 2021 14:21:06 +0000
parents e299c477b475
children 67213c4eefa6
line wrap: on
line diff
--- a/sequenza_to_hrdtools_input.R	Sun Mar 07 12:01:21 2021 +0000
+++ b/sequenza_to_hrdtools_input.R	Sun Mar 07 14:21:06 2021 +0000
@@ -1,7 +1,6 @@
+options(warn = -1)
+
 # load packages that are provided in the conda env
-options(show.error.messages = F, error = function() {
-        cat(geterrmessage(), file = stderr()); q("no", 1, F) })
-Sys.setenv(TZ = "Pacific/Auckland") # turnaround the tidyverse bug "In OlsonNames() : no Olson database found"
 
 library(optparse)
 library(tidyverse)
@@ -62,6 +61,6 @@
 print(reformatted)
 
 reformatted %>%
-  write_tsv(opt$output)
+  write.table(opt$output, quote=F, row.names=F, sep="\t")
 
 message(sprintf("Output written to %s", opt$output))