I'm trying to modify a workflow to work on list collections. Most tools work as expected without change, but I'm running into difficulty with tools that have an input with the 'multiple="true"' attribute set. For these tools, the input in question is expanded into ALL inputs in the collection, which is not the correct (in my opinion) behavior.
For example, I use BWA-MEM to map reads against a contaminant database and then Peter Cock's "filter seq by mapping" tool to discard mapped reads. This tool takes a single FASTQ file but allows multiple BAM files to filter on. It works fine for single inputs, but when a dataset collection is used upstream, it maps each FASTQ file in the collection against all BAM outputs from the previous BWA-MEM step (instead of only the BAM file resulting from mapping that specific FASTQ file).
I have no problem modifying the filtering tool (I'm running on a local instance) but I'm not sure how to get things to work nicely together. Has anyone else run into this problem?