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MALT output format options #552

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ivelsko opened this issue Sep 14, 2020 · 3 comments · Fixed by #557
Closed

MALT output format options #552

ivelsko opened this issue Sep 14, 2020 · 3 comments · Fixed by #557
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@jfy133
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enhancement New feature or request
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2.2 "Ulm"

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@ivelsko
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ivelsko commented Sep 14, 2020

Is it possible to specify the output format for MALT? I can't find it in the documentation, but I'd like to have a sam file instead of rma6. The sam file I can use with aadder from MEGAN, but not the rma6 file, and I can't find a way to convert rma6 to sam.
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jfy133 commented Sep 15, 2020

Currently, no. Good point, will add.

@jfy133 jfy133 added the enhancement New feature or request label Sep 15, 2020
@jfy133 jfy133 added this to the V2.2 "Ulm" milestone Sep 15, 2020
@jfy133 jfy133 self-assigned this Sep 15, 2020
@jfy133 jfy133 mentioned this issue Sep 15, 2020
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@jfy133 jfy133 linked a pull request Sep 15, 2020 that will close this issue
Malt sam output #557
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jfy133 commented Sep 15, 2020

Implemented, and waiting for review!

@jfy133 jfy133 closed this as completed Sep 25, 2020
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jfy133 commented Sep 25, 2020

@ivelsko merged, you can pull -r dev and it should work.

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enhancement New feature or request
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2.2 "Ulm"
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Malt sam output nf-core/eager
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@jfy133 @ivelsko