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Minimap2 enhancements #3061

Merged
merged 7 commits into from Jun 5, 2020
Merged

Minimap2 enhancements #3061

merged 7 commits into from Jun 5, 2020

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wm75
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@wm75 wm75 commented Jun 4, 2020

FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

wm75 added 7 commits June 4, 2020 13:07
@wm75
Fix -E and -O alignment options of minimap2
5600eba
@wm75
Add -C alignment option to minimap2
59c6699
@wm75
Fix minimap error handling & explicit zero values
2744390 
Catches minimap's [ERROR] messages, which indicate failure of the
tool in the pipe. Parameter defaults can now also be overwritten
with zero values, which were previously ignored. The minimum value
got increased to 1 for the -O and -E options, for which zero is
not allowed.
@wm75
Fix minimap profile selection
4dfbcdc 
Enforces sr presets for PE reads to ensure encoding of mate info in the output
FLAG field. Makes profile selection optional for single-end reads and adds
minimap's splice:hq profile as an option.
@wm75
Refactor splicing related settings
c1260e7 
Exposes more minimap2 settings related to spliced alignments, bundles
all of them inone place, and makes spliced alignment mode mutually
exclusive with --frag mode.
@wm75
Some more parameters and smaller fixes
0e0b993 
Exposes the following additional minimap2 parameters:
--max-chain-skips
--max-chain-iter
--no-end-flt

Cleanups and fixes:
- moves -G option into spliced alignment section and fixes parameter help
- reallows zeros for the second values of -O and -E
- introduces a second value for -z
@wm75
Fix documentation of paired-end alignment mode
0131a0b
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wm75 commented Jun 4, 2020

Fixes various odds and ends in the minimap2 wrapper.

@bgruening bgruening merged commit ffcf398 into galaxyproject:master Jun 5, 2020
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Thanks @wm75!

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@bgruening bgruening bgruening approved these changes

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@wm75 @bgruening