Hi I am new to galaxy, so if someone has asked this question in the past I apologize. I downloaded 42 files to galaxy via the SRA run selector as a collection. I now have my FASTQ files and would like to use Trimmomatic; however, I am above the alloted space quota. Trimmomatic was run on the first 15 files already and the rest are waiting to be processed.
My question is if I delete/purge the first 15 files in the collection ( FASTQ) will that allow Trimmoatic to resume or will it mess things up because the data is grouped together as a collection. I just not sure and it took forever to download so any advice would be much appreciated.
One solution is to break out the read data into distinct collections during download and processing in batches.
Trimmomatic creates near duplicate very large fastq outputs.
The idea would be to get through that step with a portion of the data, purge the original files, repeat with another portion, then combine the results into one collection for downstream processing.
From your description it seems like 2-4 batches would be enough.
Another is to make a small short-term extra quota request (extra 100-250 GB for a few days to a week).
This is only available for academic researchers at the public sites. How-to for accounts at UseGalaxy.org. Account quotas - Galaxy Community Hub. Make the request via email as described in that FAQ – don’t post your information here publicly.
