I have a strange behavior of tools for merging the reads (pear, FLASH). When running as a single tool on PE dataset collection is OK. But when putting it with the same option at the beginning of workflow there is an error:
cannot find 'forward' while searching for 'library.input_collection.forward'
Hi vebaev, I had the same problem so I was searching for any information, anyway it turns out you only need to specify input dataset as an individual step before the first tool in your workflow, you probably figured out since it was some time til my reply but I just wanted to leave this here for anyone who might need it.