Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

diff fastq_dump_se_render.R @ 6:4c84d748da08 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c9517f0b061cdca3b79678d9a2620e1e43115d42-dirty
author mingchen0919
date Wed, 27 Sep 2017 11:40:38 -0400
parents c9b56151f112
children 2d1c5d1633bf
line wrap: on
line diff
--- a/fastq_dump_se_render.R	Wed Sep 27 11:18:27 2017 -0400
+++ b/fastq_dump_se_render.R	Wed Sep 27 11:40:38 2017 -0400
@@ -62,13 +62,13 @@
     gsub('SRA_ACCESSION', opt$sra_accession, x)
   }) %>%
   (function(x) {
+    gsub('FORMAT', opt$format, x)
+  }) %>%
+  (function(x) {
     gsub('ECHO', opt$echo, x)
   }) %>%
   (function(x) {
-    gsub('FORMAT', opt$format, x)
-  }) %>%
-  (function(x) {
-    gsub('OUTPUT_DIR', opt$fastq_dump_se_dir, x)
+    gsub('OUTPUT_DIR', opt$output_dir, x)
   }) %>%
   (function(x) {
     fileConn = file('fastq_dump_se.Rmd')