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MALT databases are not correctly staged #501

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jfy133 opened this issue Jul 13, 2020 · 0 comments · Fixed by #502
Closed

MALT databases are not correctly staged #501

jfy133 opened this issue Jul 13, 2020 · 0 comments · Fixed by #502
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bug Something isn't working pending Addressed on branch waiting for related PR
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hackathon-tasks
Milestone
2.2 "Ulm"

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jfy133 commented Jul 13, 2020

The path is directly given to the malt command inside the process, meaning the file path is not correctly resolved unless a full path is provided. The directories should be given with the e.g. path() function.
@jfy133 jfy133 added the bug Something isn't working label Jul 13, 2020
@jfy133 jfy133 self-assigned this Jul 13, 2020
@jfy133 jfy133 added this to the V2.2 "Ulm" milestone Jul 13, 2020
@jfy133 jfy133 added this to Existing pipelines in hackathon-tasks Jul 13, 2020
@jfy133 jfy133 mentioned this issue Jul 13, 2020
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@jfy133 jfy133 linked a pull request Jul 13, 2020 that will close this issue
Fix MALT staging and simplify unmapped read treatment #502
Merged
8 tasks
@jfy133 jfy133 added the pending Addressed on branch waiting for related PR label Jul 13, 2020
@jfy133 jfy133 closed this as completed Jul 15, 2020
hackathon-tasks automation moved this from Existing pipelines to Done Jul 15, 2020
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bug Something isn't working pending Addressed on branch waiting for related PR
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hackathon-tasks
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2.2 "Ulm"
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Fix MALT staging and simplify unmapped read treatment nf-core/eager
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@jfy133