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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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Minimap2: Paired ends option faulty #2432

Open darkskiez opened 5 years ago

darkskiez commented 5 years ago

Even when you choose paired end data files this is not passed to minimap2 correctly.

https://github.com/lh3/minimap2#map-short-accurate-genomic-reads

"Two reads are considered to be paired if they are adjacent in the input stream and have the same name (with the /[0-9] suffix trimmed if present)."

I had thought it was a file naming issue in galaxy with the dat file renaming, but I think from my understanding of the minimap code only the sr mapping mode supports paired ends, so this option should only be available when that mapping is selected if you can confirm my suspicions.

https://github.com/lh3/minimap2/blob/6762368cf0fdee289f757abb267e7ed43867ed52/options.c#L108

mvdbeek commented 5 years ago

That's for interleaved streams.

minimap2 -ax sr ref.fa read1.fq read2.fq > aln.sam     # paired-end alignment

Is what's implemented in the wrapper.

only the sr mapping mode supports paired ends, so this option should only be available when that mapping is selected if you can confirm my suspicions

That's right, we could do that. I don't think you'd accidentally select long read mapping presets with paired end options though, but if you want to implement this why not.

darkskiez commented 5 years ago

Yes I had accidentally selected the wrong mode (not sr) but could still select paired end data files, that should be blocked or highlighted for an improved user experience.

mvdbeek commented 5 years ago

fair enough