The task was to download several SRAs from NCBI, align to reference genome, find SNPs. I made many attempts to use collections in workflow, but it broke at some point. When I tried to figure out the cause of it I come to following observation: when I use BWA-MEM manually, point it to "list of pairs" collection and reference genome FAS, it works. But if I make a simple test workflow with only BWA-MEM step, and use the same files upon run, it does not appear in History, and nothing happened. Is it bug, or am I doing something wrong?
Several of your mini-workflows do not include an Inputs dataset. I do see Inputs included in the larger workflows.
Try adding one in, connect it to the downstream tool or tools, and rerun. Choices for Inputs types are at the very top of the tool panel within the workflow editor.
- Input dataset
- Input dataset collection
This may be a bug - I am checking with the development team. Not including Inputs will work for individual datasets when selected at runtime, but not collections datasets. If we make an issue ticket, I'll link it back as a comment.
There is another issue with workflows related to tool version conflicts we are working on. The workaround (until fixed) is to connect all noodles for tools in the editor left-to-right (input noodles, then output noodles, per tool). This may have been part of your problem with the larger workflow. Try reconnecting the noodles in this way and the version problem will not be a factor when you are tuning/troubleshooting the larger workflow.
Thank for reporting the problem! Jen, Galaxy team
Thank you Jen!
I've figured out the problem with left-to-right connections, and I override it using copying of the downstream blocks and reconnecting, it's OK. But I tried to use input for BWA-MEM, and I cannot connect the "Input dataset collection" to "Select a paired collection", it does not turn green. If I select other types of the input, then I could connect, but it does not work the way I would like, of course. And as I said, manually I do the same BWA-MEM on collections, and it works perfectly.