Revamp of metagenomics rules #927
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Fixes #777. |
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Do we know how this fares with single-end read BAM input? #820 |
dpark01
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Feb 20, 2019
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Since this heavily relies on yesimon-specific forks of krakenuniq and kaiju, can you send us links to the code diffs between the forks and the upstream/authoritative? In your github I see forks where your master branches have not diverged from the upstream master branches, so I assume the magic is all in one of the named branches of each repo?
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The fork of krakenuniq is the The fork of kaiju is minor and is in the |
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Add support for krakenuniq, kaiju to replace kraken and diamond in default pipelines. Both rely on customized krakenuniq/kaiju packages for custom functionality, like loading database from pipe or printing out all taxa hits (kaiju). Krona fixed to use hit counts as scores in report files directly, instead of counting the individual read classifications (which takes a long time).
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Incorporated in #944 |
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Add support for krakenuniq, kaiju to replace kraken and diamond in default pipelines.
Both rely on customized krakenuniq/kaiju packages for custom functionality, like loading database
from pipe or printing out all taxa hits (kaiju).
Krona fixed to use hit counts as scores in report files directly, instead of counting the
individual read classifications (which takes a long time).
Includes changes from #915 and also some pytest deprecation fixes:
s/log.warn(/log.warning(/,runslowcommand line configuration.