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Initial commit of a functional optitype script #625

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merged 2 commits into from
Apr 23, 2019

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johnegarza
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This is the first commit of our combined optitype prep step and optitype run step for HLA-typing. There are a few issues to discuss, documented in the issues beginning at genome/docker-immuno_tools-cwl#1. In the interest of time, the current form of the script will be added to our repo, then updated after discussion.

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@tmooney tmooney left a comment

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+1, there are definitely things to change about /usr/bin/optitype_script.sh, but that's beyond the scope of this PR.

definitions/tools/optitype_dna.cwl Outdated Show resolved Hide resolved
@johnegarza johnegarza merged commit afdce1a into genome:master Apr 23, 2019
@johnegarza johnegarza deleted the initial_optitype branch April 23, 2019 19:17
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