yuch7 / cwlexec

A new open source tool to run CWL workflows on LSF
Other
36 stars 8 forks source link

Collecting output for an array of glob patterns based on inputs fails #14

Closed biokcb closed 6 years ago

biokcb commented 6 years ago

Hi,

We have a simple example that takes a string as input and outputs two files with names based on the input string. When using glob to find both files based on the name pattern $(inputs.name)_1.txt and $(inputs.name)_2.txt, the glob seems to interpret these as literal strings rather than evaluating $(inputs.name) in each case:

outfile.txt

182   "outputBinding" : {
183     "glob" : {
184       "patterns" : [ "$(inputs.name)_1.txt", "$(inputs.name)_2.txt" ],

then returns:

218 {
219   "out_file" : [ ]
220 }

If $(inputs.name) is changed to the exact string, it works, but it should evaluate these for pattern matching.

GlobOutputArrayError.tar.gz

skeeey commented 6 years ago

Yes, the pattern expression is not handled, fixed at 4fedf26