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Lofreq fixes #4626

Merged
merged 4 commits into from
Jul 6, 2022
Merged

Lofreq fixes #4626

merged 4 commits into from
Jul 6, 2022

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bernt-matthias
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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)

@bernt-matthias
lofreq indelqual: set ftype in tests
efa6736 
otherwise the files are compared as binary
@bernt-matthias
lofreq alnqual: set ftype
53fd5a3 
otherwise bam files are compared binary
@bernt-matthias
lofreq call: fix tests
0e1193b
@bernt-matthias
fix test assertions
26c1c43
@bernt-matthias bernt-matthias requested a review from mvdbeek July 5, 2022 09:22
@bernt-matthias bernt-matthias mentioned this pull request Jul 5, 2022
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@bernt-matthias bernt-matthias marked this pull request as draft July 5, 2022 13:44
@bernt-matthias
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Making this a draft. Maybe the addition of ftype is not necessary, xref galaxyproject/galaxy#14261

@mvdbeek
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mvdbeek commented Jul 5, 2022

Let's merge this ? I don't see a problem, pretty sure that's been that way.

@bernt-matthias bernt-matthias marked this pull request as ready for review July 6, 2022 09:03
@bernt-matthias
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You are right: https://github.com/galaxyproject/galaxy/blob/613b0788928d43df54b8b82518478a4981d25e9e/lib/galaxy/tool_util/verify/__init__.py#L143

@bernt-matthias bernt-matthias merged commit 3751719 into galaxyproject:master Jul 6, 2022
@bernt-matthias bernt-matthias deleted the lofreq-fixes branch July 6, 2022 09:04
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@bgruening bgruening bgruening approved these changes

@mvdbeek mvdbeek Awaiting requested review from mvdbeek

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@bernt-matthias @mvdbeek @bgruening