Hello, it seems I used to be able to run Spades on trimmed fastq files in batch mode, but now that option seems to be gone on both the .eu and the .org servers.
My recollection is that I could add the files manually to a batch mode option, or submit a collection where the files would be processed individually. Now Spades only will consider multiple single end files to be part of the same sample.
I have 96 barcoded amplicon sequencing fastq files (generated with nanopore sequencing) I’d like to batch process in Spades and would like to not have to submit 96 separate jobs. Thanks.
Try an early version of SPAdes, for example, Galaxy Version 3.12.0. It creates separate assembly for every input file. It takes SE reads, just leave the second input box for R reads empty.
Users can select another version of a tool during job setup via Version (three blocks) icon in the top right corner of the middle window.
Maybe consider using Unicycler. It uses SPAdes and can handle SE data. It produces separate assemblies when multiple files are selected.
Kind regards,
Igor
You can also stick with the current version of SPAdes, but you need to provide your data as a nested list. That is each of your 96 samples would be an element of the outer list and contain a list with a single dataset each (could be several of course).
This will create 96 SPAdes job wwith each one handling the data from the inner list.
Update: I was able to run in a batch mode by making a workflow that took single fastq data files and selecting by hand each of the 96 files when I ran the workflow. Not perfect, but OK for what I need to do.