Closed drjrm3 closed 5 years ago
@drjrm3 the root cause is still the inputs.R1_file
(split_reads/read1_file
) is an array, this because output_file
does not participate in scatter, we use the original inputs value to build the javascript context.
For scatter case, we may need to build the javascript context after the scatter phase. I will try to fix this problem
Working on #34 again and I can now reproduce the same error in my larger workflow.
Step 1 is
split_reads
which correctly scatters over the files now after the workaround proposed.Step 2 scatters over those files and tries to generate a string for
output_file
from one of the files generated as part of step 1. I am using the following JavaScript to generate this string and it works incwltool
so I had assumed it was the correct approach:However, the error I get with cwlexec is:
so it looks like it is not correctly using
inputs.R1_file
. Am I using the correct approach here? It appears to be the same general issues as in #34 but I don't know that I can use the same workaround since I don't take anything in theinputs
section in the scatter so I can't use that assource
.UndefinedVariableError.tar.gz