Description
Describe the bug
When testing BRC-Analytics.org functionality and trying to run the "Single-Cell RNA-seq Preprocessing: 10X Genomics CellPlex Multiplexed Samples" workflow (https://iwc.galaxyproject.org/workflow/fastq-to-matrix-10x-scrna-seq-fastq-to-matrix-10x-cellplex/) it failed on 7th step of the linked history, "RNA STARSolo on data 5, data 4, and others" with an error that indicated that it ran out of memory and suggested providing a flag to increase the amount of memory used to sort the bam file:
EXITING because of fatal ERROR: not enough memory for BAM sorting:
SOLUTION: re-run STAR with at least --limitBAMsortRAM 29816090916
Jun 06 17:15:02 ...... FATAL ERROR, exiting
However, there isn't an option in the UI to provide this flag, so there is no way to run this step in Galaxy, regardless of the workflow.
My suggestion (which echos @mvdbeek 's) is to allow this step to not sort the BAM but rather sort it in a subsequent step with samtools.
Galaxy Version and/or server at which you observed the bug
Galaxy Version: {"version_major":"25.0","version_minor":"rc1"}
Browser and Operating System
Operating System: macOS 15.5
Browser: Safari
To Reproduce
In this history: https://usegalaxy.org/u/scottcain/h/t-brucie-cell-cycle
See step 7.