Closed bearbob closed 8 years ago
Since the error occurs in the refactoring phase of a foreign task, it would help to also see the rest of the workflow.
The error hasn't shown up since. Hope this helps somehow, nonetheless. rnaVC2.txt
Ran into the same issue just today. This minimal script reproduces the bug:
deftask cat( out( File ) : <lst( File )> ) in bash *{
out=out.txt
cat ${lst[@]} > $out
}*
x = "a.txt" "a.txt";
cat( lst: x );
The problem is, that if a.txt is staged in twice, it already exists the second time effi tries to create a link in the directory. That's why you got the eexist error.
Fixed the bug in effi.
I have a workflow with the file definition: fq1 = "files/ext_L6918-1_JH-1_S6_R1_001.fastq"; fq2 = "files/ext_L6918-1_JH-1_S6_R1_001.fastq";
By accident, these names happen to be the same file, which (seems) to trigger the following error:
After changing the filename it works again. Also, when I had the same file but as a .gz it also worked.