Hi @jlocker
You don’t need to run the FastqGroomer tool for any short reads that are from an Illumina 1.7 or later sequencing pipeline. Meaning, you can skip this tool entirely and save processing time.
→ Instead, just load up the files and let Galaxy autodetect the datatype (includes quality score scaling detection for fastq datasets). The guess should be fastqsanger or fastqsangergz. If you don’t have that detected, it means more in going on: truncated or corrupt file is the usual reason. Getting Data into Galaxy
For the TrimGalore step, do you mean that the datasets are queued (gray in color)? That is normal when working at a public Galaxy server. Some of your jobs run, some of other people’s jobs run, more of yours, repeat.
Next time, the good way to get SRA data into Galaxy is with the tool Faster Download and Extract Reads in FASTQ format from NCBI SRA. Input the accessions and use all defaults. You can use a list of accessions for batches.
And, you could consider using a workflow. Even if this is just for those two tools – put both into a workflow, start it up, and set a notification. Everything will stream and process while you are away, including the download step.
You can extract that workflow from a history you already have, or use a template from the GTN, or create from scratch. The workflow editor looks much like the regular analysis view and all of the same options are available. Find the tool in the workflow tool panel, add it to the canvas, set parameters, and connect the input.
The quality control workflow here is a good template. You can swap out tools and fully customize. Hands-on: Quality Control / Sequence analysis
Hope this helps! Please explain more if I am misunderstanding 