I was wondering how I could setup a workflow to iterate through a list of FASTA files, in addition to a list of pairs (PE Illumina reads), and run a tool (bowtie2 for alignment) so that the first FASTA file is used with the first pair of reads, second FASTA file used for second pair of reads, and so on. I’ve attached some screenshots below with my current history structure for reference.
I couldn’t find any way to loop through collections (ideally using a “for”-style of loop). Closest i could find was the “Extract Dataset” tool which requires you enter an index; so this would become a pretty manual process if I were to do this for all 30+ items spread over 2 lists.
Just wanting to make sure that there is no way to do this within Galaxy already before I go out and start programming a custom tool for this.
Thanks in advance!