HISAT2 Data manager reports unrecognized arguments for SNP annotation

[jennaj]

HISAT2 DM has a problem with advanced options re SNP annotation. Wrapper needs update? See: unrecognized arguments

Fatal error: Exit code 2 ()
usage: extract_snps.py [-h] [-v] [--testset] [genome_file] [snp_file]
extract_snps.py: error: unrecognized arguments: --genome_file --snp_file snps.tabular

[jennaj]

Comment .. this DM fails when incorporating ref annotation even for very small genomes and given 64 GB. Has anyone does this successfully?

There is also some confustion about inputs. The form could have updated help text for SNP and Splices to help with usage (exact expected input dataset format).

Examples:

• What exact SNP format for input (full UCSC table?)? Seems like best, tried others, all failed to be recognized (what the ticket is primarily about)
• Form suggests that GFF/GTF is loaded by a DM (Likely could just use better phrasing). However, in testing, it does use this input from a dataset in the history loaded by the user. This has been confusing for even advanced admins.
• If that GFF/GTF dataset is in another history (not the admin DM history), it might be good to copy it over to the DM history much like the workflow function "send results to another history" moves over inputs. (reproducibility/inputs tracking). Consider doing same for SNP dataset when this functional.

[bgruening]

@davebx can you please look at it?