Mercurial > repos > lecorguille > xcms_fillpeaks

diff lib.r @ 22:6824468351ca draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author lecorguille
date Mon, 29 Apr 2019 06:31:04 -0400
parents c0e7d2fae9ee
children 999f9db0ca2c
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line diff
--- a/lib.r	Tue Apr 09 12:23:16 2019 -0400
+++ b/lib.r	Mon Apr 29 06:31:04 2019 -0400
@@ -333,7 +333,7 @@
     files[exists] <- sub("//","/",files[exists])
 
     # WHAT IS ON THE FILESYSTEM
-    filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
+    filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
     filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
 
     # COMPARISON